rs10513957

Variant names:

• chr18-69221200-G-C
• rs10513957

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 0.102 in 152,208 control chromosomes in the GnomAD database, including 864 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 0.10 (864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 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: 0.102 AC: 15579 AN: 152088 Hom.: 863 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.0965

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.0887

Gnomad SAS AF: 0.0975

Gnomad FIN AF: 0.0868

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0967

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.102 AC: 15596 AN: 152208 Hom.: 864 Cov.: 32 AF XY: 0.103 AC XY: 7656 AN XY: 74420

African (AFR) AF: 0.120 AC: 4972 AN: 41532

American (AMR) AF: 0.0963 AC: 1473 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0928 AC: 322 AN: 3468

East Asian (EAS) AF: 0.0889 AC: 460 AN: 5176

South Asian (SAS) AF: 0.0976 AC: 471 AN: 4826

European-Finnish (FIN) AF: 0.0868 AC: 919 AN: 10592

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0967 AC: 6578 AN: 68004

Other (OTH) AF: 0.124 AC: 262 AN: 2112

Alfa AF: 0.0988 Hom.: 92

Bravo AF: 0.104

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.68
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs10513957; hg19: chr18-66888437;