6-31110718-C-G

Variant names:

• chr6-31110718-C-G
• rs1265059

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 0.528 in 152,048 control chromosomes in the GnomAD database, including 21,177 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 0.53 (21177 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.572 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: 0.528 AC: 80267 AN: 151930 Hom.: 21161 Cov.: 33

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.528 AC: 80319 AN: 152048 Hom.: 21177 Cov.: 33 AF XY: 0.526 AC XY: 39112 AN XY: 74334

African (AFR) AF: 0.545 AC: 22606 AN: 41454

American (AMR) AF: 0.521 AC: 7968 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2418 AN: 3472

East Asian (EAS) AF: 0.473 AC: 2447 AN: 5172

South Asian (SAS) AF: 0.590 AC: 2847 AN: 4826

European-Finnish (FIN) AF: 0.506 AC: 5347 AN: 10566

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34849 AN: 67966

Other (OTH) AF: 0.562 AC: 1183 AN: 2106

Alfa AF: 0.357 Hom.: 840

Bravo AF: 0.528

Asia WGS AF: 0.526 AC: 1833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.1
DANN	Benign	0.63
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs1265059; hg19: chr6-31078495;