rs10738147

Variant names:

• chr9-1012154-T-C
• rs10738147

Your query was ambiguous. Multiple possible variants found:

• chr9-1012154-T-C
• chr9-1012154-T-G

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 0.643 in 152,116 control chromosomes in the GnomAD database, including 32,434 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 0.64 (32434 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 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: 0.643 AC: 97701 AN: 151998 Hom.: 32393 Cov.: 33

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.643 AC: 97803 AN: 152116 Hom.: 32434 Cov.: 33 AF XY: 0.642 AC XY: 47746 AN XY: 74350

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.589

Alfa AF: 0.594 Hom.: 29477

Bravo AF: 0.642

Asia WGS AF: 0.492 AC: 1716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.1
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10738147; hg19: chr9-1012154;