rs1041296

Positions:

• chr10-130204767-A-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 0.163 in 152,210 control chromosomes in the GnomAD database, including 3,097 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 0.16 (3097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 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: 0.162 AC: 24695 AN: 152090 Hom.: 3083 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.0982

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0645

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0890

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.163 AC: 24749 AN: 152210 Hom.: 3097 Cov.: 32 AF XY: 0.159 AC XY: 11815 AN XY: 74434

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.0980

Gnomad4 ASJ AF: 0.0971

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0645

Gnomad4 NFE AF: 0.0890

Gnomad4 OTH AF: 0.143

Alfa AF: 0.124 Hom.: 595

Bravo AF: 0.172

Asia WGS AF: 0.190 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1041296; hg19: chr10-132003031;