rs10499197

chr6-137811379-T-G

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 0.0237 in 152,382 control chromosomes in the GnomAD database, including 47 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 0.024 (47 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0237 (3610/152382) while in subpopulation SAS AF= 0.0493 (238/4832). AF 95% confidence interval is 0.0441. There are 47 homozygotes in gnomad4. There are 1721 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 47 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: 0.0237 AC: 3608 AN: 152264 Hom.: 47 Cov.: 33

Gnomad AFR AF: 0.0174

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0197

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.0486

Gnomad FIN AF: 0.0161

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0281

Gnomad OTH AF: 0.0201

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

GnomAD4 genome AF: 0.0237 AC: 3610 AN: 152382 Hom.: 47 Cov.: 33 AF XY: 0.0231 AC XY: 1721 AN XY: 74522

Gnomad4 AFR AF: 0.0173

Gnomad4 AMR AF: 0.0197

Gnomad4 ASJ AF: 0.0435

Gnomad4 EAS AF: 0.0129

Gnomad4 SAS AF: 0.0493

Gnomad4 FIN AF: 0.0161

Gnomad4 NFE AF: 0.0281

Gnomad4 OTH AF: 0.0208

Alfa AF: 0.0275 Hom.: 20

Bravo AF: 0.0223

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	1.1
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499197; hg19: chr6-138132516;