4-71052133-A-T

Variant names:

• chr4-71052133-A-T
• rs10518082

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 0.776 in 152,102 control chromosomes in the GnomAD database, including 45,989 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 0.78 (45989 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 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: 0.776 AC: 117931 AN: 151984 Hom.: 45944 Cov.: 32

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.776 AC: 118029 AN: 152102 Hom.: 45989 Cov.: 32 AF XY: 0.773 AC XY: 57447 AN XY: 74334

African (AFR) AF: 0.842 AC: 34947 AN: 41492

American (AMR) AF: 0.835 AC: 12766 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2785 AN: 3470

East Asian (EAS) AF: 0.836 AC: 4317 AN: 5164

South Asian (SAS) AF: 0.731 AC: 3526 AN: 4826

European-Finnish (FIN) AF: 0.647 AC: 6822 AN: 10540

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50370 AN: 68006

Other (OTH) AF: 0.795 AC: 1680 AN: 2114

Alfa AF: 0.756 Hom.: 5393

Bravo AF: 0.792

Asia WGS AF: 0.767 AC: 2669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.3
DANN	Benign	0.67
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10518082; hg19: chr4-71917850;