10-17488514-G-C

Position:

• chr10-17488514-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0315 in 152,072 control chromosomes in the GnomAD database, including 115 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 0.032 (115 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.878

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0315 (4793/152072) while in subpopulation AMR AF= 0.0475 (727/15296). AF 95% confidence interval is 0.0447. There are 115 homozygotes in gnomad4. There are 2472 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 115 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: 0.0315 AC: 4788 AN: 151954 Hom.: 115 Cov.: 32

Gnomad AFR AF: 0.00903

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0472

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.00808

Gnomad FIN AF: 0.0899

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0379

Gnomad OTH AF: 0.0211

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

GnomAD4 genome AF: 0.0315 AC: 4793 AN: 152072 Hom.: 115 Cov.: 32 AF XY: 0.0333 AC XY: 2472 AN XY: 74334

Gnomad4 AFR AF: 0.00900

Gnomad4 AMR AF: 0.0475

Gnomad4 ASJ AF: 0.0179

Gnomad4 EAS AF: 0.00405

Gnomad4 SAS AF: 0.00830

Gnomad4 FIN AF: 0.0899

Gnomad4 NFE AF: 0.0379

Gnomad4 OTH AF: 0.0208

Alfa AF: 0.000813 Hom.: 0

Bravo AF: 0.0296

Asia WGS AF: 0.00953 AC: 33 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1937353; hg19: chr10-17530513;