chr6-117200993-C-G

Variant names:

• chr6-117200993-C-G
• rs961764

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 0.586 in 151,992 control chromosomes in the GnomAD database, including 26,432 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 0.59 (26432 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 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: 0.586 AC: 88996 AN: 151874 Hom.: 26403 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.586 AC: 89077 AN: 151992 Hom.: 26432 Cov.: 32 AF XY: 0.584 AC XY: 43351 AN XY: 74274

African (AFR) AF: 0.640 AC: 26503 AN: 41436

American (AMR) AF: 0.532 AC: 8127 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2047 AN: 3470

East Asian (EAS) AF: 0.694 AC: 3594 AN: 5176

South Asian (SAS) AF: 0.338 AC: 1630 AN: 4822

European-Finnish (FIN) AF: 0.574 AC: 6050 AN: 10548

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39337 AN: 67952

Other (OTH) AF: 0.583 AC: 1231 AN: 2110

Alfa AF: 0.487 Hom.: 1416

Bravo AF: 0.589

Asia WGS AF: 0.516 AC: 1792 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.38
DANN	Benign	0.37
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs961764; hg19: chr6-117522156; COSMIC: COSV69421934;