rs6456042

Variant names:

• chr6-166121254-A-C
• rs6456042

Your query was ambiguous. Multiple possible variants found:

• chr6-166121254-A-C
• chr6-166121254-A-G
• chr6-166121254-A-T

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 151,936 control chromosomes in the GnomAD database, including 30,878 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 0.64 (30878 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 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: 96416 AN: 151818 Hom.: 30855 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.635 AC: 96491 AN: 151936 Hom.: 30878 Cov.: 32 AF XY: 0.637 AC XY: 47278 AN XY: 74266

African (AFR) AF: 0.632 AC: 26178 AN: 41436

American (AMR) AF: 0.719 AC: 10976 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2247 AN: 3468

East Asian (EAS) AF: 0.901 AC: 4665 AN: 5178

South Asian (SAS) AF: 0.626 AC: 3010 AN: 4806

European-Finnish (FIN) AF: 0.576 AC: 6049 AN: 10510

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

European-Non Finnish (NFE) AF: 0.608 AC: 41317 AN: 67952

Other (OTH) AF: 0.651 AC: 1377 AN: 2114

Alfa AF: 0.633 Hom.: 25676

Bravo AF: 0.652

Asia WGS AF: 0.775 AC: 2693 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	3.3
DANN	Benign	0.55
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs6456042; hg19: chr6-166534742;