chr10-87977344-G-A

Variant names:

• chr10-87977344-G-A
• rs17346680

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The variant allele was found at a frequency of 0.0219 in 151,658 control chromosomes in the GnomAD database, including 58 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 0.022 (58 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.918
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0219 (3327/151658) while in subpopulation NFE AF = 0.0375 (2544/67894). AF 95% confidence interval is 0.0363. There are 58 homozygotes in GnomAd4. There are 1531 alleles in the male GnomAd4 subpopulation. Median coverage is 30. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 58 gene

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: 0.0220 AC: 3330 AN: 151540 Hom.: 58 Cov.: 30

Gnomad AFR AF: 0.00621

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0134

Gnomad ASJ AF: 0.0182

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00480

Gnomad FIN AF: 0.0166

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0375

Gnomad OTH AF: 0.0149

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

GnomAD4 genome AF: 0.0219 AC: 3327 AN: 151658 Hom.: 58 Cov.: 30 AF XY: 0.0207 AC XY: 1531 AN XY: 74074

African (AFR) AF: 0.00620 AC: 256 AN: 41318

American (AMR) AF: 0.0134 AC: 204 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.0182 AC: 63 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00460 AC: 22 AN: 4784

European-Finnish (FIN) AF: 0.0166 AC: 174 AN: 10502

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0375 AC: 2544 AN: 67894

Other (OTH) AF: 0.0148 AC: 31 AN: 2098

Alfa AF: 0.0345 Hom.: 50

Bravo AF: 0.0219

Asia WGS AF: 0.00404 AC: 14 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	14
DANN	Benign	0.86
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs17346680; hg19: chr10-89737101;