rs10518072

chr4-70224941-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.119 in 151,980 control chromosomes in the GnomAD database, including 1,192 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 0.12 (1192 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.761

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18153 AN: 151862 Hom.: 1192 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.0610

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.119 AC: 18154 AN: 151980 Hom.: 1192 Cov.: 31 AF XY: 0.120 AC XY: 8896 AN XY: 74290

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0607

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.110

Alfa AF: 0.129 Hom.: 1143

Bravo AF: 0.124

Asia WGS AF: 0.0290 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.73
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518072; hg19: chr4-71090658;