10-107616211-T-A

Position:

• chr10-107616211-T-A

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 0.447 in 151,914 control chromosomes in the GnomAD database, including 15,743 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 0.45 (15743 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67977 AN: 151796 Hom.: 15746 Cov.: 31

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.447 AC: 67979 AN: 151914 Hom.: 15743 Cov.: 31 AF XY: 0.443 AC XY: 32872 AN XY: 74254

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.452

Alfa AF: 0.482 Hom.: 2250

Bravo AF: 0.442

Asia WGS AF: 0.261 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2099803; hg19: chr10-109375969;