rs11596974

Variant names:

• chr10-18131455-G-A
• rs11596974

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 0.243 in 152,010 control chromosomes in the GnomAD database, including 4,796 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 0.24 (4796 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.34 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: 0.243 AC: 36876 AN: 151890 Hom.: 4774 Cov.: 33

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.243 AC: 36942 AN: 152010 Hom.: 4796 Cov.: 33 AF XY: 0.252 AC XY: 18719 AN XY: 74290

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.252

Alfa AF: 0.228 Hom.: 6918

Bravo AF: 0.235

Asia WGS AF: 0.252 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.0
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11596974; hg19: chr10-18420384;