rs1415916

Variant names:

• chr10-81565807-A-T
• rs1415916

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 0.0669 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.170 AC: 7036 AN: 41426

American (AMR) AF: 0.0360 AC: 548 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3464

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5180

South Asian (SAS) AF: 0.0228 AC: 110 AN: 4824

European-Finnish (FIN) AF: 0.0127 AC: 132 AN: 10432

Middle Eastern (MID) AF: 0.0333 AC: 9 AN: 270

European-Non Finnish (NFE) AF: 0.0317 AC: 2148 AN: 67740

Other (OTH) AF: 0.0422 AC: 89 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.69
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1415916; hg19: chr10-83325563;