6-110523056-A-G

Variant names:

• chr6-110523056-A-G
• rs2817778

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 0.923 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.970 AC: 40303 AN: 41562

American (AMR) AF: 0.938 AC: 14356 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3291 AN: 3470

East Asian (EAS) AF: 0.848 AC: 4396 AN: 5182

South Asian (SAS) AF: 0.898 AC: 4332 AN: 4826

European-Finnish (FIN) AF: 0.869 AC: 9222 AN: 10608

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61604 AN: 68024

Other (OTH) AF: 0.940 AC: 1989 AN: 2116

Alfa AF: 0.912 Hom.: 242589

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
PhyloP100		-0.069

Splicing

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

Other links and lift over

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