rs6785504

Variant names:

• chr3-152954990-G-T
• rs6785504

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 0.517 in 152,044 control chromosomes in the GnomAD database, including 20,626 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 0.52 (20626 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78478 AN: 151926 Hom.: 20574 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.517 AC: 78599 AN: 152044 Hom.: 20626 Cov.: 32 AF XY: 0.517 AC XY: 38456 AN XY: 74316

African (AFR) AF: 0.588 AC: 24392 AN: 41486

American (AMR) AF: 0.551 AC: 8415 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1929 AN: 3466

East Asian (EAS) AF: 0.509 AC: 2634 AN: 5176

South Asian (SAS) AF: 0.501 AC: 2422 AN: 4830

European-Finnish (FIN) AF: 0.470 AC: 4957 AN: 10554

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32157 AN: 67936

Other (OTH) AF: 0.500 AC: 1055 AN: 2108

Alfa AF: 0.489 Hom.: 64606

Bravo AF: 0.525

Asia WGS AF: 0.557 AC: 1936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
DANN	Benign	0.39
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6785504; hg19: chr3-152672779;