10-17488514-G-C

Variant names:

• chr10-17488514-G-C
• rs1937353

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• 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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 115 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.00900 AC: 374 AN: 41548

American (AMR) AF: 0.0475 AC: 727 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0179 AC: 62 AN: 3466

East Asian (EAS) AF: 0.00405 AC: 21 AN: 5186

South Asian (SAS) AF: 0.00830 AC: 40 AN: 4822

European-Finnish (FIN) AF: 0.0899 AC: 947 AN: 10538

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0379 AC: 2575 AN: 67900

Other (OTH) AF: 0.0208 AC: 44 AN: 2112

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
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs1937353; hg19: chr10-17530513;