6-137816414-C-T

Variant names:

• chr6-137816414-C-T
• rs679670

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 0.56 in 151,970 control chromosomes in the GnomAD database, including 25,373 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 0.56 (25373 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 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: 0.560 AC: 85039 AN: 151852 Hom.: 25371 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.560 AC: 85052 AN: 151970 Hom.: 25373 Cov.: 32 AF XY: 0.562 AC XY: 41761 AN XY: 74282

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.585

Alfa AF: 0.617 Hom.: 43437

Bravo AF: 0.557

Asia WGS AF: 0.697 AC: 2426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0030
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: rs679670; hg19: chr6-138137551; COSMIC: COSV60285802;