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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000508616.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251088	ENST00000508616.1	TSL:1	n.26+2536T>C		intron	N/A
	ENSG00000300508	ENST00000772455.1		n.271+662A>G		intron	N/A
	ENSG00000300508	ENST00000772456.1		n.259+662A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1497536;

hg19: chr3-97955056;