rs10499372

Positions:

• chr7-10438859-C-T

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 0.0465 in 152,160 control chromosomes in the GnomAD database, including 174 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 0.047 (174 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0465 (7079/152160) while in subpopulation AFR AF= 0.0511 (2123/41518). AF 95% confidence interval is 0.0493. There are 174 homozygotes in gnomad4. There are 3392 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 174 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0465 AC: 7072 AN: 152044 Hom.: 174 Cov.: 32

Gnomad AFR AF: 0.0511

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0343

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.0356

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0490

Gnomad OTH AF: 0.0479

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

GnomAD4 genome AF: 0.0465 AC: 7079 AN: 152160 Hom.: 174 Cov.: 32 AF XY: 0.0456 AC XY: 3392 AN XY: 74400

Gnomad4 AFR AF: 0.0511

Gnomad4 AMR AF: 0.0343

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0292

Gnomad4 FIN AF: 0.0356

Gnomad4 NFE AF: 0.0490

Gnomad4 OTH AF: 0.0479

Alfa AF: 0.0491 Hom.: 21

Bravo AF: 0.0474

Asia WGS AF: 0.0170 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.9
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499372; hg19: chr7-10478486;