10-95071632-C-T

Variant names:

• chr10-95071632-C-T
• rs1557044

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 0.83 in 152,124 control chromosomes in the GnomAD database, including 52,838 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 0.83 (52838 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.857 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: 0.830 AC: 126230 AN: 152006 Hom.: 52788 Cov.: 32

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.973

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.830 AC: 126334 AN: 152124 Hom.: 52838 Cov.: 32 AF XY: 0.828 AC XY: 61568 AN XY: 74364

African (AFR) AF: 0.825 AC: 34228 AN: 41498

American (AMR) AF: 0.760 AC: 11605 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2929 AN: 3472

East Asian (EAS) AF: 0.542 AC: 2800 AN: 5168

South Asian (SAS) AF: 0.810 AC: 3905 AN: 4820

European-Finnish (FIN) AF: 0.880 AC: 9322 AN: 10598

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.863 AC: 58681 AN: 67978

Other (OTH) AF: 0.823 AC: 1738 AN: 2112

Alfa AF: 0.848 Hom.: 206182

Bravo AF: 0.817

Asia WGS AF: 0.699 AC: 2432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.31
DANN	Benign	0.17
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1557044; hg19: chr10-96831389;