chr10-81060627-T-C

Variant names:

• chr10-81060627-T-C
• rs17703918

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 0.0404 in 152,136 control chromosomes in the GnomAD database, including 178 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 0.040 (178 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.055 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0404 AC: 6146 AN: 152024 Hom.: 177 Cov.: 32

Gnomad AFR AF: 0.00984

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0337

Gnomad ASJ AF: 0.0407

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.0996

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.0444

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

GnomAD4 genome AF: 0.0404 AC: 6147 AN: 152136 Hom.: 178 Cov.: 32 AF XY: 0.0414 AC XY: 3078 AN XY: 74400

African (AFR) AF: 0.00982 AC: 408 AN: 41566

American (AMR) AF: 0.0337 AC: 514 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0407 AC: 141 AN: 3468

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5170

South Asian (SAS) AF: 0.0116 AC: 56 AN: 4826

European-Finnish (FIN) AF: 0.0996 AC: 1053 AN: 10568

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0565 AC: 3840 AN: 67966

Other (OTH) AF: 0.0435 AC: 92 AN: 2114

Alfa AF: 0.0440 Hom.: 61

Bravo AF: 0.0347

Asia WGS AF: 0.00982 AC: 34 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.82
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs17703918; hg19: chr10-82820383;