rs6917113

Variant names:

• chr6-169109322-T-A
• rs6917113

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 0.199 in 151,980 control chromosomes in the GnomAD database, including 3,488 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 0.20 (3488 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 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: 0.199 AC: 30165 AN: 151862 Hom.: 3471 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0884

Gnomad SAS AF: 0.0869

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.199 AC: 30226 AN: 151980 Hom.: 3488 Cov.: 32 AF XY: 0.196 AC XY: 14557 AN XY: 74262

African (AFR) AF: 0.310 AC: 12844 AN: 41462

American (AMR) AF: 0.126 AC: 1919 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 451 AN: 3470

East Asian (EAS) AF: 0.0886 AC: 453 AN: 5110

South Asian (SAS) AF: 0.0884 AC: 426 AN: 4818

European-Finnish (FIN) AF: 0.188 AC: 1988 AN: 10564

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11646 AN: 67956

Other (OTH) AF: 0.164 AC: 345 AN: 2110

Alfa AF: 0.198 Hom.: 420

Bravo AF: 0.201

Asia WGS AF: 0.102 AC: 357 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.22
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs6917113; hg19: chr6-169509417;