4-62512548-T-G

Variant names:

• chr4-62512548-T-G
• rs13126803

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 0.147 in 151,958 control chromosomes in the GnomAD database, including 1,733 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 0.15 (1733 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 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: 0.147 AC: 22308 AN: 151840 Hom.: 1731 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.0972

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.147 AC: 22326 AN: 151958 Hom.: 1733 Cov.: 31 AF XY: 0.147 AC XY: 10903 AN XY: 74256

African (AFR) AF: 0.160 AC: 6634 AN: 41414

American (AMR) AF: 0.0970 AC: 1481 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 955 AN: 3466

East Asian (EAS) AF: 0.0177 AC: 91 AN: 5130

South Asian (SAS) AF: 0.142 AC: 682 AN: 4810

European-Finnish (FIN) AF: 0.184 AC: 1943 AN: 10572

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9951 AN: 67980

Other (OTH) AF: 0.164 AC: 345 AN: 2108

Alfa AF: 0.142 Hom.: 7488

Bravo AF: 0.140

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.1
DANN	Benign	0.29
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs13126803; hg19: chr4-63378266;