rs6820763

Variant names:

• chr4-27789962-C-A
• rs6820763

Your query was ambiguous. Multiple possible variants found:

• chr4-27789962-C-A
• chr4-27789962-C-G
• chr4-27789962-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 0.196 in 152,086 control chromosomes in the GnomAD database, including 3,543 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 0.20 (3543 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 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: 0.196 AC: 29729 AN: 151968 Hom.: 3540 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.196 AC: 29751 AN: 152086 Hom.: 3543 Cov.: 32 AF XY: 0.199 AC XY: 14772 AN XY: 74362

African (AFR) AF: 0.247 AC: 10247 AN: 41450

American (AMR) AF: 0.213 AC: 3257 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3468

East Asian (EAS) AF: 0.573 AC: 2963 AN: 5170

South Asian (SAS) AF: 0.125 AC: 604 AN: 4824

European-Finnish (FIN) AF: 0.207 AC: 2193 AN: 10582

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9635 AN: 67994

Other (OTH) AF: 0.153 AC: 322 AN: 2106

Alfa AF: 0.159 Hom.: 1065

Bravo AF: 0.207

Asia WGS AF: 0.332 AC: 1152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.36
DANN	Benign	0.39
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs6820763; hg19: chr4-27791584;