rs10518182

Variant names:

• chr4-77835861-T-G
• rs10518182

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 0.184 in 152,192 control chromosomes in the GnomAD database, including 2,970 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 0.18 (2970 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 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: 0.184 AC: 27942 AN: 152074 Hom.: 2969 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.0173

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.184 AC: 27955 AN: 152192 Hom.: 2970 Cov.: 32 AF XY: 0.182 AC XY: 13539 AN XY: 74392

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.0171

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.213

Alfa AF: 0.223 Hom.: 5652

Bravo AF: 0.175

Asia WGS AF: 0.0880 AC: 307 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.9
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518182; hg19: chr4-78757015;