rs10499197

Variant names:

• chr6-137811379-T-G
• rs10499197
• ENST00000834747.1:n.-200T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000834747.1(ENSG00000308524):​n.-200T>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. 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: ENSG00000308524 ENST00000834747.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188
• Publications: 29 publications found

Genes affected

ENSG00000308524 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 47 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
ENSG00000308524	ENST00000834747.1	n.-200T>G		upstream_gene_variant

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

African (AFR) AF: 0.0173 AC: 720 AN: 41592

American (AMR) AF: 0.0197 AC: 302 AN: 15314

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 151 AN: 3470

East Asian (EAS) AF: 0.0129 AC: 67 AN: 5192

South Asian (SAS) AF: 0.0493 AC: 238 AN: 4832

European-Finnish (FIN) AF: 0.0161 AC: 171 AN: 10624

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0281 AC: 1912 AN: 68038

Other (OTH) AF: 0.0208 AC: 44 AN: 2114

Alfa AF: 0.0285 Hom.: 93

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
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs10499197; hg19: chr6-138132516;