rs262119

Variant names:

• chr6-142521656-T-C
• rs262119

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 0.441 in 152,034 control chromosomes in the GnomAD database, including 18,086 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 0.44 (18086 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66861 AN: 151916 Hom.: 18037 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.441 AC: 66972 AN: 152034 Hom.: 18086 Cov.: 32 AF XY: 0.437 AC XY: 32508 AN XY: 74322

African (AFR) AF: 0.773 AC: 32040 AN: 41466

American (AMR) AF: 0.381 AC: 5825 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1249 AN: 3472

East Asian (EAS) AF: 0.359 AC: 1859 AN: 5174

South Asian (SAS) AF: 0.350 AC: 1689 AN: 4822

European-Finnish (FIN) AF: 0.267 AC: 2824 AN: 10566

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20131 AN: 67946

Other (OTH) AF: 0.459 AC: 967 AN: 2108

Alfa AF: 0.434 Hom.: 3213

Bravo AF: 0.461

Asia WGS AF: 0.422 AC: 1468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.67
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs262119; hg19: chr6-142842793;