10-57964643-A-T

Variant names:

• chr10-57964643-A-T
• rs7088591

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 0.0917 in 152,192 control chromosomes in the GnomAD database, including 905 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 0.092 (905 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.688
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 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: 0.0917 AC: 13942 AN: 152074 Hom.: 904 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.0763

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.0367

Gnomad SAS AF: 0.0551

Gnomad FIN AF: 0.0132

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0619

Gnomad OTH AF: 0.0950

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

GnomAD4 genome AF: 0.0917 AC: 13955 AN: 152192 Hom.: 905 Cov.: 31 AF XY: 0.0898 AC XY: 6679 AN XY: 74410

African (AFR) AF: 0.178 AC: 7392 AN: 41532

American (AMR) AF: 0.0761 AC: 1162 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0876 AC: 304 AN: 3470

East Asian (EAS) AF: 0.0366 AC: 189 AN: 5166

South Asian (SAS) AF: 0.0554 AC: 267 AN: 4822

European-Finnish (FIN) AF: 0.0132 AC: 140 AN: 10618

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0620 AC: 4213 AN: 67994

Other (OTH) AF: 0.0940 AC: 199 AN: 2116

Alfa AF: 0.0692 Hom.: 71

Bravo AF: 0.101

Asia WGS AF: 0.0490 AC: 173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.9
DANN	Benign	0.74
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs7088591; hg19: chr10-59724403;