rs10518072

Variant names:

• chr4-70224941-T-C
• rs10518072

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 0.119 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.106 AC: 4396 AN: 41512

American (AMR) AF: 0.190 AC: 2884 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 397 AN: 3462

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5158

South Asian (SAS) AF: 0.0607 AC: 293 AN: 4830

European-Finnish (FIN) AF: 0.121 AC: 1284 AN: 10610

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8601 AN: 67912

Other (OTH) AF: 0.110 AC: 231 AN: 2102

Alfa AF: 0.126 Hom.: 1541

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
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs10518072; hg19: chr4-71090658;