ENST00000436015.6:n.*231-1734C>A

Variant names:

• chr9-5883409-G-T
• rs10733517
• ENST00000436015.6:n.*231-1734C>A

Variant summary

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

The ENST00000436015.6(BRD10):​n.*231-1734C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.977 in 151,098 control chromosomes in the GnomAD database, including 72,279 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 0.98 (72279 hom., cov: 26)
• Consequence: BRD10 ENST00000436015.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 1 publications found

Genes affected

BRD10 (HGNC:23378): (bromodomain containing 10)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.986 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000436015.6. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRD10	ENST00000436015.6	TSL:3	n.*231-1734C>A		intron	N/A	ENSP00000438370.1

Frequencies

GnomAD3 genomes AF: 0.977 AC: 147572 AN: 150982 Hom.: 72225 Cov.: 26

Gnomad AFR AF: 0.975

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.992

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.981

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.977 AC: 147685 AN: 151098 Hom.: 72279 Cov.: 26 AF XY: 0.975 AC XY: 71853 AN XY: 73698

African (AFR) AF: 0.975 AC: 40094 AN: 41122

American (AMR) AF: 0.992 AC: 15024 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3423 AN: 3466

East Asian (EAS) AF: 0.795 AC: 4068 AN: 5116

South Asian (SAS) AF: 0.926 AC: 4439 AN: 4796

European-Finnish (FIN) AF: 0.980 AC: 9971 AN: 10176

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.992 AC: 67404 AN: 67956

Other (OTH) AF: 0.978 AC: 2061 AN: 2108

Alfa AF: 0.985 Hom.: 97314

Bravo AF: 0.979

Asia WGS AF: 0.859 AC: 2988 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.20
DANN	Benign	0.75
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs10733517; hg19: chr9-5883409;