6-138110216-T-C

Variant names:

• chr6-138110216-T-C
• rs9494941

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 0.45 in 152,018 control chromosomes in the GnomAD database, including 15,775 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 0.45 (15775 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 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: 0.450 AC: 68315 AN: 151900 Hom.: 15749 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.450 AC: 68374 AN: 152018 Hom.: 15775 Cov.: 32 AF XY: 0.451 AC XY: 33541 AN XY: 74308

African (AFR) AF: 0.511 AC: 21185 AN: 41432

American (AMR) AF: 0.425 AC: 6495 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1348 AN: 3464

East Asian (EAS) AF: 0.723 AC: 3740 AN: 5176

South Asian (SAS) AF: 0.532 AC: 2564 AN: 4816

European-Finnish (FIN) AF: 0.423 AC: 4469 AN: 10558

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27330 AN: 67978

Other (OTH) AF: 0.421 AC: 891 AN: 2114

Alfa AF: 0.405 Hom.: 22871

Bravo AF: 0.450

Asia WGS AF: 0.616 AC: 2140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.71
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9494941; hg19: chr6-138431353;