rs1497536

Variant names:

• chr3-98236212-T-C
• rs1497536
• ENST00000508616.1:n.26+2536T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-98236212-T-C
• chr3-98236212-T-G

Variant summary

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

The ENST00000508616.1(ENSG00000251088):​n.26+2536T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,180 control chromosomes in the GnomAD database, including 2,805 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 0.11 (2805 hom., cov: 33)
• Consequence: ENSG00000251088 ENST00000508616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 1 publications found

Genes affected

ENSG00000251088 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929320	XR_924257.1	n.263-364A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251088	ENST00000508616.1	n.26+2536T>C		intron_variant	Intron 1 of 3	1
ENSG00000300508	ENST00000772455.1	n.271+662A>G		intron_variant	Intron 2 of 2
ENSG00000300508	ENST00000772456.1	n.259+662A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16329 AN: 152062 Hom.: 2792 Cov.: 33

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0481

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.000942

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00231

Gnomad OTH AF: 0.0948

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

GnomAD4 genome AF: 0.108 AC: 16383 AN: 152180 Hom.: 2805 Cov.: 33 AF XY: 0.105 AC XY: 7813 AN XY: 74412

African (AFR) AF: 0.364 AC: 15086 AN: 41492

American (AMR) AF: 0.0480 AC: 734 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.00104 AC: 5 AN: 4824

European-Finnish (FIN) AF: 0.000942 AC: 10 AN: 10620

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.00231 AC: 157 AN: 67994

Other (OTH) AF: 0.0938 AC: 198 AN: 2110

Alfa AF: 0.0806 Hom.: 300

Bravo AF: 0.123

Asia WGS AF: 0.0240 AC: 82 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	4.8
DANN	Benign	0.80
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1497536; hg19: chr3-97955056;