chr6-131764261-C-T

Position:

• chr6-131764261-C-T

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 0.142 in 152,168 control chromosomes in the GnomAD database, including 2,097 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 0.14 (2097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21630 AN: 152050 Hom.: 2091 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.0866

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.142 AC: 21667 AN: 152168 Hom.: 2097 Cov.: 32 AF XY: 0.146 AC XY: 10873 AN XY: 74392

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.0866

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.136

Alfa AF: 0.123 Hom.: 577

Bravo AF: 0.155

Asia WGS AF: 0.298 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.25
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10452621; hg19: chr6-132085401;