6-137816414-C-T

Variant names:

• chr6-137816414-C-T
• rs679670

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 0.56 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.342 AC: 14181 AN: 41442

American (AMR) AF: 0.648 AC: 9886 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2129 AN: 3466

East Asian (EAS) AF: 0.869 AC: 4493 AN: 5170

South Asian (SAS) AF: 0.694 AC: 3347 AN: 4820

European-Finnish (FIN) AF: 0.591 AC: 6224 AN: 10532

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42780 AN: 67958

Other (OTH) AF: 0.585 AC: 1236 AN: 2112

Alfa AF: 0.608 Hom.: 99504

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
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs679670; hg19: chr6-138137551; COSMIC: COSV60285802;