rs9494895

Variant names:

• chr6-137913641-C-T
• rs9494895

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 0.0566 in 152,058 control chromosomes in the GnomAD database, including 396 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 0.057 (396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.124 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: 0.0565 AC: 8592 AN: 151940 Hom.: 395 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0343

Gnomad ASJ AF: 0.0404

Gnomad EAS AF: 0.0422

Gnomad SAS AF: 0.0369

Gnomad FIN AF: 0.0166

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0294

Gnomad OTH AF: 0.0479

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

GnomAD4 genome AF: 0.0566 AC: 8609 AN: 152058 Hom.: 396 Cov.: 32 AF XY: 0.0549 AC XY: 4079 AN XY: 74352

African (AFR) AF: 0.127 AC: 5262 AN: 41490

American (AMR) AF: 0.0344 AC: 525 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0404 AC: 140 AN: 3464

East Asian (EAS) AF: 0.0427 AC: 221 AN: 5174

South Asian (SAS) AF: 0.0366 AC: 176 AN: 4814

European-Finnish (FIN) AF: 0.0166 AC: 175 AN: 10564

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0294 AC: 1995 AN: 67962

Other (OTH) AF: 0.0484 AC: 102 AN: 2108

Alfa AF: 0.0498 Hom.: 43

Bravo AF: 0.0602

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.50
DANN	Benign	0.58
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs9494895; hg19: chr6-138234778;