chr6-137913641-C-T

Variant names:

• chr6-137913641-C-T
• rs9494895

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 0.0566 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0344

Gnomad4 ASJ AF: 0.0404

Gnomad4 EAS AF: 0.0427

Gnomad4 SAS AF: 0.0366

Gnomad4 FIN AF: 0.0166

Gnomad4 NFE AF: 0.0294

Gnomad4 OTH AF: 0.0484

Alfa AF: 0.0467 Hom.: 32

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9494895; hg19: chr6-138234778;