chr4-22329842-A-C

Variant names:

• chr4-22329842-A-C
• rs2270851
• ENST00000510705.3:n.1386A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000510705.3(ENSG00000250039):​n.1386A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,878 control chromosomes in the GnomAD database, including 3,994 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.22 (3994 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENSG00000250039 ENST00000510705.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 0 publications found

Genes affected

ENSG00000250039 (HGNC:58742):

ENSG00000309702 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510705.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC100505912	NR_037877.1		n.362+15T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250039	ENST00000510705.3	TSL:5	n.1386A>C		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000309702	ENST00000843176.1		n.424+15T>G		intron	N/A
	ENSG00000309702	ENST00000843177.1		n.428+15T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34057 AN: 151756 Hom.: 3992 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.243

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.224 AC: 34080 AN: 151876 Hom.: 3994 Cov.: 31 AF XY: 0.227 AC XY: 16850 AN XY: 74222

African (AFR) AF: 0.219 AC: 9059 AN: 41408

American (AMR) AF: 0.269 AC: 4100 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 959 AN: 3466

East Asian (EAS) AF: 0.323 AC: 1651 AN: 5118

South Asian (SAS) AF: 0.372 AC: 1785 AN: 4794

European-Finnish (FIN) AF: 0.180 AC: 1903 AN: 10568

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.202 AC: 13709 AN: 67960

Other (OTH) AF: 0.243 AC: 509 AN: 2096

Alfa AF: 0.211 Hom.: 1849

Bravo AF: 0.233

Asia WGS AF: 0.331 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.13
DANN	Benign	0.40
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2270851; hg19: chr4-22331465;