rs6917113

Positions:

• chr6-169109322-T-A

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 0.199 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.0886

Gnomad4 SAS AF: 0.0884

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.164

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6917113; hg19: chr6-169509417;