10-101073307-T-C

Variant names:

• chr10-101073307-T-C
• rs807013

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 0.77 in 152,066 control chromosomes in the GnomAD database, including 45,392 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 0.77 (45392 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.849 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: 0.770 AC: 116946 AN: 151948 Hom.: 45349 Cov.: 31

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.770 AC: 117039 AN: 152066 Hom.: 45392 Cov.: 31 AF XY: 0.763 AC XY: 56736 AN XY: 74336

African (AFR) AF: 0.856 AC: 35531 AN: 41490

American (AMR) AF: 0.737 AC: 11265 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2733 AN: 3470

East Asian (EAS) AF: 0.565 AC: 2916 AN: 5164

South Asian (SAS) AF: 0.668 AC: 3217 AN: 4814

European-Finnish (FIN) AF: 0.711 AC: 7517 AN: 10572

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51252 AN: 67960

Other (OTH) AF: 0.778 AC: 1641 AN: 2108

Alfa AF: 0.759 Hom.: 136529

Bravo AF: 0.775

Asia WGS AF: 0.667 AC: 2317 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	9.5
DANN	Benign	0.61
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs807013; hg19: chr10-102833064;