10-81413053-T-C

Variant names:

• chr10-81413053-T-C
• rs1576305

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 0.918 in 152,006 control chromosomes in the GnomAD database, including 64,127 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 0.92 (64127 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.953 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: 0.918 AC: 139387 AN: 151888 Hom.: 64069 Cov.: 31

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.918 AC: 139504 AN: 152006 Hom.: 64127 Cov.: 31 AF XY: 0.919 AC XY: 68252 AN XY: 74274

African (AFR) AF: 0.961 AC: 39885 AN: 41496

American (AMR) AF: 0.929 AC: 14149 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3164 AN: 3468

East Asian (EAS) AF: 0.953 AC: 4920 AN: 5160

South Asian (SAS) AF: 0.927 AC: 4468 AN: 4818

European-Finnish (FIN) AF: 0.929 AC: 9822 AN: 10576

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.884 AC: 60047 AN: 67936

Other (OTH) AF: 0.913 AC: 1927 AN: 2110

Alfa AF: 0.908 Hom.: 8104

Bravo AF: 0.919

Asia WGS AF: 0.957 AC: 3326 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.60
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs1576305; hg19: chr10-83172809;