rs7150062

Variant names:

• chr14-54460932-A-G
• rs7150062

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 0.198 in 152,166 control chromosomes in the GnomAD database, including 3,524 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 0.20 (3524 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 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: 0.198 AC: 30083 AN: 152048 Hom.: 3515 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.198 AC: 30147 AN: 152166 Hom.: 3524 Cov.: 32 AF XY: 0.194 AC XY: 14441 AN XY: 74402

African (AFR) AF: 0.322 AC: 13344 AN: 41470

American (AMR) AF: 0.172 AC: 2631 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0893 AC: 310 AN: 3470

East Asian (EAS) AF: 0.104 AC: 540 AN: 5188

South Asian (SAS) AF: 0.162 AC: 782 AN: 4832

European-Finnish (FIN) AF: 0.138 AC: 1456 AN: 10584

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10618 AN: 68006

Other (OTH) AF: 0.161 AC: 340 AN: 2114

Alfa AF: 0.166 Hom.: 1451

Bravo AF: 0.206

Asia WGS AF: 0.156 AC: 544 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	0.57
DANN	Benign	0.37
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7150062; hg19: chr14-54927650;