rs1415916

Positions:

• chr10-81565807-A-T

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 0.0669 in 151,582 control chromosomes in the GnomAD database, including 644 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 0.067 (644 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 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: 0.0668 AC: 10120 AN: 151464 Hom.: 642 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0361

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.0310

Gnomad NFE AF: 0.0317

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0669 AC: 10135 AN: 151582 Hom.: 644 Cov.: 32 AF XY: 0.0634 AC XY: 4701 AN XY: 74112

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.0360

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0228

Gnomad4 FIN AF: 0.0127

Gnomad4 NFE AF: 0.0317

Gnomad4 OTH AF: 0.0422

Alfa AF: 0.0546 Hom.: 59

Bravo AF: 0.0711

Asia WGS AF: 0.0180 AC: 62 AN: 3398

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1415916; hg19: chr10-83325563;