10-93155858-T-C

Variant names:

• chr10-93155858-T-C
• rs1339822

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 0.589 in 152,004 control chromosomes in the GnomAD database, including 27,016 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 0.59 (27016 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 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: 0.589 AC: 89412 AN: 151886 Hom.: 26974 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.589 AC: 89514 AN: 152004 Hom.: 27016 Cov.: 32 AF XY: 0.594 AC XY: 44159 AN XY: 74280

African (AFR) AF: 0.582 AC: 24100 AN: 41440

American (AMR) AF: 0.650 AC: 9934 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1785 AN: 3472

East Asian (EAS) AF: 0.982 AC: 5092 AN: 5184

South Asian (SAS) AF: 0.745 AC: 3585 AN: 4810

European-Finnish (FIN) AF: 0.574 AC: 6057 AN: 10550

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36914 AN: 67960

Other (OTH) AF: 0.582 AC: 1230 AN: 2112

Alfa AF: 0.562 Hom.: 12476

Bravo AF: 0.598

Asia WGS AF: 0.849 AC: 2953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.060
DANN	Benign	0.39
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1339822; hg19: chr10-94915615;