rs2817778

Variant names:

• chr6-110523056-A-G
• rs2817778

Your query was ambiguous. Multiple possible variants found:

• chr6-110523056-A-G
• chr6-110523056-A-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 0.923 in 152,302 control chromosomes in the GnomAD database, including 64,980 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 0.92 (64980 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.962 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: 0.923 AC: 140470 AN: 152184 Hom.: 64923 Cov.: 33

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.939

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

GnomAD4 genome AF: 0.923 AC: 140585 AN: 152302 Hom.: 64980 Cov.: 33 AF XY: 0.919 AC XY: 68476 AN XY: 74478

Gnomad4 AFR AF: 0.970

Gnomad4 AMR AF: 0.938

Gnomad4 ASJ AF: 0.948

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.898

Gnomad4 FIN AF: 0.869

Gnomad4 NFE AF: 0.906

Gnomad4 OTH AF: 0.940

Alfa AF: 0.912 Hom.: 105741

Bravo AF: 0.932

Asia WGS AF: 0.901 AC: 3132 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2817778; hg19: chr6-110844259; COSMIC: COSV60266210;