rs10435736

Positions:

• chr9-31419917-G-C
• chr9-31419917-G-T

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 0.175 in 152,038 control chromosomes in the GnomAD database, including 2,528 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 (2528 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.457

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26597 AN: 151922 Hom.: 2518 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.175 AC: 26645 AN: 152038 Hom.: 2528 Cov.: 32 AF XY: 0.179 AC XY: 13265 AN XY: 74296

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.178

Alfa AF: 0.157 Hom.: 232

Bravo AF: 0.186

Asia WGS AF: 0.253 AC: 877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10435736; hg19: chr9-31419915;