rs3763338

Variant names:

• chr6-28926534-G-A
• rs3763338

Your query was ambiguous. Multiple possible variants found:

• chr6-28926534-G-A
• chr6-28926534-G-C
• chr6-28926534-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.109 in 152,226 control chromosomes in the GnomAD database, including 1,013 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 0.11 (1013 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 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: 0.109 AC: 16547 AN: 152108 Hom.: 1011 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0810

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0895

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.109 AC: 16576 AN: 152226 Hom.: 1013 Cov.: 32 AF XY: 0.109 AC XY: 8145 AN XY: 74418

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.0810

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.0896

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0947 Hom.: 434

Bravo AF: 0.115

Asia WGS AF: 0.0770 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3763338; hg19: chr6-28894311;