rs142330712

Variant names:

• chr22-49774254-G-A
• rs142330712
• NM_001304808.3:c.3549C>T

Your query was ambiguous. Multiple possible variants found:

• chr22-49774254-G-A
• chr22-49774254-G-C

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_001304808.3(BRD1):​c.3549C>T​(p.Ser1183Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000202 in 1,613,850 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00096 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00012 (0 hom.)
• Consequence: BRD1 NM_001304808.3 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0710
• Publications: 0 publications found

Genes affected

BRD1 (HGNC:1102): (bromodomain containing 1) This gene encodes a bromodomain-containing protein that localizes to the nucleus and can interact with DNA and histone tails. The encoded protein is a component of the MOZ/MORF acetyltransferase complex and can stimulate acetylation of histones H3 and H4, thereby potentially playing a role in gene activation. Variation in this gene is associated with schizophrenia and bipolar disorder in some study populations. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2017]

ACMG classification

Our verdict: Benign. The variant received -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BP6: Variant 22-49774254-G-A is Benign according to our data. Variant chr22-49774254-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 722639.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.071 with no splicing effect.
• BS2: High AC in GnomAd4 at 146 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304808.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRD1	NM_001304808.3	MANE Select	c.3549C>T	p.Ser1183Ser	synonymous	Exon 13 of 13	NP_001291737.1	O95696-2
	BRD1	NM_001394548.1		c.3543C>T	p.Ser1181Ser	synonymous	Exon 13 of 13	NP_001381477.1
	BRD1	NM_001349941.2		c.3534C>T	p.Ser1178Ser	synonymous	Exon 13 of 13	NP_001336870.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRD1	ENST00000404760.6	TSL:2 MANE Select	c.3549C>T	p.Ser1183Ser	synonymous	Exon 13 of 13	ENSP00000385858.1	O95696-2
	BRD1	ENST00000216267.12	TSL:1	c.3156C>T	p.Ser1052Ser	synonymous	Exon 12 of 12	ENSP00000216267.8	O95696-1
	BRD1	ENST00000404034.5	TSL:1	c.3156C>T	p.Ser1052Ser	synonymous	Exon 13 of 13	ENSP00000384076.1	O95696-1

Frequencies

GnomAD3 genomes AF: 0.000952 AC: 145 AN: 152232 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00316

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000393

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.000957

GnomAD2 exomes AF: 0.000275 AC: 69 AN: 250686 AF XY: 0.000251

Gnomad AFR exome AF: 0.00277

Gnomad AMR exome AF: 0.000145

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000531

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000123 AC: 180 AN: 1461500 Hom.: 0 Cov.: 30 AF XY: 0.000120 AC XY: 87 AN XY: 726990

African (AFR) AF: 0.00290 AC: 97 AN: 33468

American (AMR) AF: 0.0000671 AC: 3 AN: 44692

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26134

East Asian (EAS) AF: 0.00 AC: 0 AN: 39684

South Asian (SAS) AF: 0.000348 AC: 30 AN: 86240

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53354

Middle Eastern (MID) AF: 0.000174 AC: 1 AN: 5748

European-Non Finnish (NFE) AF: 0.0000279 AC: 31 AN: 1111802

Other (OTH) AF: 0.000298 AC: 18 AN: 60378

GnomAD4 genome AF: 0.000958 AC: 146 AN: 152350 Hom.: 0 Cov.: 33 AF XY: 0.000993 AC XY: 74 AN XY: 74496

African (AFR) AF: 0.00317 AC: 132 AN: 41584

American (AMR) AF: 0.000392 AC: 6 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.000622 AC: 3 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10626

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000441 AC: 3 AN: 68040

Other (OTH) AF: 0.000947 AC: 2 AN: 2112

Alfa AF: 0.000458 Hom.: 1

Bravo AF: 0.00116

EpiCase AF: 0.0000545

EpiControl AF: 0.000119

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	6.1
DANN	Benign	0.87
PhyloP100		-0.071

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs142330712; hg19: chr22-50167902;