rs6798732

Variant names:

• chr3-87632881-C-A
• rs6798732

Your query was ambiguous. Multiple possible variants found:

• chr3-87632881-C-A
• chr3-87632881-C-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 0.453 in 151,630 control chromosomes in the GnomAD database, including 16,904 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 0.45 (16904 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 2 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 = 0.647 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: 0.453 AC: 68620 AN: 151512 Hom.: 16862 Cov.: 31

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.391

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.453 AC: 68712 AN: 151630 Hom.: 16904 Cov.: 31 AF XY: 0.453 AC XY: 33581 AN XY: 74060

African (AFR) AF: 0.653 AC: 27026 AN: 41362

American (AMR) AF: 0.368 AC: 5609 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1262 AN: 3470

East Asian (EAS) AF: 0.502 AC: 2571 AN: 5126

South Asian (SAS) AF: 0.320 AC: 1536 AN: 4796

European-Finnish (FIN) AF: 0.397 AC: 4160 AN: 10470

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.370 AC: 25115 AN: 67864

Other (OTH) AF: 0.449 AC: 946 AN: 2106

Alfa AF: 0.396 Hom.: 39400

Bravo AF: 0.461

Asia WGS AF: 0.412 AC: 1431 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.3
DANN	Benign	0.77
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs6798732; hg19: chr3-87682031;