10-101073307-T-C

Variant names:

• chr10-101073307-T-C
• rs807013

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.778

Alfa AF: 0.754 Hom.: 87342

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs807013; hg19: chr10-102833064;