rs17346680

Positions:

• chr10-87977344-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 58 gene

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: 0.0220 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

Gnomad4 AFR AF: 0.00620

Gnomad4 AMR AF: 0.0134

Gnomad4 ASJ AF: 0.0182

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00460

Gnomad4 FIN AF: 0.0166

Gnomad4 NFE AF: 0.0375

Gnomad4 OTH AF: 0.0148

Alfa AF: 0.0326 Hom.: 20

Bravo AF: 0.0219

Asia WGS AF: 0.00404 AC: 14 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17346680; hg19: chr10-89737101;