rs1041296

Variant names:

• chr10-130204767-A-G
• rs1041296

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.346 AC: 14376 AN: 41490

American (AMR) AF: 0.0980 AC: 1499 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0971 AC: 337 AN: 3472

East Asian (EAS) AF: 0.169 AC: 876 AN: 5182

South Asian (SAS) AF: 0.107 AC: 515 AN: 4832

European-Finnish (FIN) AF: 0.0645 AC: 684 AN: 10612

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0890 AC: 6056 AN: 68016

Other (OTH) AF: 0.143 AC: 302 AN: 2112

Alfa AF: 0.124 Hom.: 2935

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
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1041296; hg19: chr10-132003031;