rs936534

Variant names:

• chr2-70347761-A-G
• rs936534

Your query was ambiguous. Multiple possible variants found:

• chr2-70347761-A-G
• chr2-70347761-A-T

Variant summary

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

The variant allele was found at a frequency of 0.5 in 152,070 control chromosomes in the GnomAD database, including 20,421 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 0.50 (20421 hom., cov: 32)
• Consequence: BRD7P6 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455
• Publications: 2 publications found

Genes affected

BRD7P6 (HGNC:37632): (bromodomain containing 7 pseudogene 6)

ENSG00000297954 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRD7P6		n.70347761A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297954	ENST00000752023.1	n.118-3330T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75948 AN: 151952 Hom.: 20374 Cov.: 32

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.500 AC: 76058 AN: 152070 Hom.: 20421 Cov.: 32 AF XY: 0.505 AC XY: 37521 AN XY: 74310

African (AFR) AF: 0.700 AC: 29057 AN: 41484

American (AMR) AF: 0.481 AC: 7354 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1472 AN: 3470

East Asian (EAS) AF: 0.570 AC: 2946 AN: 5172

South Asian (SAS) AF: 0.433 AC: 2085 AN: 4818

European-Finnish (FIN) AF: 0.512 AC: 5406 AN: 10564

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.389 AC: 26429 AN: 67966

Other (OTH) AF: 0.481 AC: 1013 AN: 2106

Alfa AF: 0.457 Hom.: 4237

Bravo AF: 0.514

Asia WGS AF: 0.528 AC: 1834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.7
DANN	Benign	0.82
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs936534; hg19: chr2-70574893;