rs10009955

chr4-152739255-C-Achr4-152739255-C-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 0.668 in 151,942 control chromosomes in the GnomAD database, including 34,131 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 0.67 (34131 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101356 AN: 151824 Hom.: 34082 Cov.: 30

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.668 AC: 101461 AN: 151942 Hom.: 34131 Cov.: 30 AF XY: 0.671 AC XY: 49822 AN XY: 74262

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.648

Alfa AF: 0.634 Hom.: 28462

Bravo AF: 0.675

Asia WGS AF: 0.739 AC: 2569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.13
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10009955; hg19: chr4-153660407;