chr6-142476152-G-A

Variant names:

• chr6-142476152-G-A
• rs7763064

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 0.381 in 151,972 control chromosomes in the GnomAD database, including 12,123 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 0.38 (12123 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 45 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.562 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: 0.381 AC: 57820 AN: 151854 Hom.: 12094 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.381 AC: 57905 AN: 151972 Hom.: 12123 Cov.: 32 AF XY: 0.379 AC XY: 28128 AN XY: 74282

African (AFR) AF: 0.569 AC: 23549 AN: 41418

American (AMR) AF: 0.356 AC: 5430 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1163 AN: 3472

East Asian (EAS) AF: 0.353 AC: 1821 AN: 5156

South Asian (SAS) AF: 0.320 AC: 1545 AN: 4822

European-Finnish (FIN) AF: 0.264 AC: 2791 AN: 10562

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20338 AN: 67952

Other (OTH) AF: 0.418 AC: 882 AN: 2110

Alfa AF: 0.328 Hom.: 26280

Bravo AF: 0.393

Asia WGS AF: 0.403 AC: 1399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.67
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7763064; hg19: chr6-142797289;