6-166149366-T-C

Variant names:

• chr6-166149366-T-C
• rs3127441

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 0.675 in 152,044 control chromosomes in the GnomAD database, including 35,435 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 0.68 (35435 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 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: 0.675 AC: 102592 AN: 151926 Hom.: 35396 Cov.: 31

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.675 AC: 102693 AN: 152044 Hom.: 35435 Cov.: 31 AF XY: 0.673 AC XY: 49983 AN XY: 74308

African (AFR) AF: 0.813 AC: 33731 AN: 41472

American (AMR) AF: 0.644 AC: 9848 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2327 AN: 3470

East Asian (EAS) AF: 0.860 AC: 4438 AN: 5158

South Asian (SAS) AF: 0.634 AC: 3056 AN: 4818

European-Finnish (FIN) AF: 0.543 AC: 5725 AN: 10546

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41438 AN: 67982

Other (OTH) AF: 0.685 AC: 1445 AN: 2110

Alfa AF: 0.645 Hom.: 3968

Bravo AF: 0.693

Asia WGS AF: 0.770 AC: 2677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.64
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs3127441; hg19: chr6-166562854;