6-166122073-C-T

Variant names:

• chr6-166122073-C-T
• rs3127412

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 0.635 in 152,076 control chromosomes in the GnomAD database, including 30,881 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 0.63 (30881 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 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: 0.635 AC: 96456 AN: 151958 Hom.: 30858 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.635 AC: 96531 AN: 152076 Hom.: 30881 Cov.: 32 AF XY: 0.636 AC XY: 47302 AN XY: 74344

African (AFR) AF: 0.632 AC: 26212 AN: 41496

American (AMR) AF: 0.719 AC: 10993 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2250 AN: 3470

East Asian (EAS) AF: 0.902 AC: 4656 AN: 5164

South Asian (SAS) AF: 0.627 AC: 3019 AN: 4818

European-Finnish (FIN) AF: 0.575 AC: 6077 AN: 10572

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41275 AN: 67958

Other (OTH) AF: 0.653 AC: 1377 AN: 2110

Alfa AF: 0.636 Hom.: 5410

Bravo AF: 0.652

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.54
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs3127412; hg19: chr6-166535561; COSMIC: COSV50467526;