rs7503953

Variant names:

• chr17-6238357-A-C
• rs7503953
• ENST00000761409.1:n.152+237T>G

Your query was ambiguous. Multiple possible variants found:

• chr17-6238357-A-C
• chr17-6238357-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000761409.1(ENSG00000299170):​n.152+237T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,044 control chromosomes in the GnomAD database, including 49,382 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 0.80 (49382 hom., cov: 33)
• Consequence: ENSG00000299170 ENST00000761409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 12 publications found

Genes affected

ENSG00000299170 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903904	XR_007065593.1	n.-205A>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299170	ENST00000761409.1	n.152+237T>G		intron_variant	Intron 1 of 1
ENSG00000299154	ENST00000761288.1	n.-126A>C		upstream_gene_variant
ENSG00000299154	ENST00000761289.1	n.-72A>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122262 AN: 151926 Hom.: 49343 Cov.: 33

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.904

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.805 AC: 122355 AN: 152044 Hom.: 49382 Cov.: 33 AF XY: 0.801 AC XY: 59507 AN XY: 74308

African (AFR) AF: 0.781 AC: 32404 AN: 41478

American (AMR) AF: 0.788 AC: 12034 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2905 AN: 3466

East Asian (EAS) AF: 0.737 AC: 3782 AN: 5134

South Asian (SAS) AF: 0.690 AC: 3325 AN: 4822

European-Finnish (FIN) AF: 0.777 AC: 8203 AN: 10552

Middle Eastern (MID) AF: 0.890 AC: 260 AN: 292

European-Non Finnish (NFE) AF: 0.836 AC: 56844 AN: 68016

Other (OTH) AF: 0.828 AC: 1748 AN: 2110

Alfa AF: 0.823 Hom.: 30757

Bravo AF: 0.807

Asia WGS AF: 0.736 AC: 2559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.5
DANN	Benign	0.73
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs7503953; hg19: chr17-6141677;