rs9416026

Variant names:

• chr10-72657743-T-C
• rs9416026

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 0.456 in 150,430 control chromosomes in the GnomAD database, including 19,863 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 0.46 (19863 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.664 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: 0.456 AC: 68561 AN: 150310 Hom.: 19866 Cov.: 27

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.0402

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.587

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.456 AC: 68548 AN: 150430 Hom.: 19863 Cov.: 27 AF XY: 0.443 AC XY: 32420 AN XY: 73188

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.0401

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.488

Alfa AF: 0.555 Hom.: 3291

Bravo AF: 0.439

Asia WGS AF: 0.210 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9416026; hg19: chr10-74417501;