chr6-166180964-T-A

Position:

• chr6-166180964-T-A

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 0.535 in 152,136 control chromosomes in the GnomAD database, including 22,411 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 0.53 (22411 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.817

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81266 AN: 152018 Hom.: 22391 Cov.: 33

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.535 AC: 81326 AN: 152136 Hom.: 22411 Cov.: 33 AF XY: 0.524 AC XY: 38984 AN XY: 74392

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.530

Alfa AF: 0.561 Hom.: 2976

Bravo AF: 0.533

Asia WGS AF: 0.328 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6924357; hg19: chr6-166594452; COSMIC: COSV60302332;