rs13098279

Variant names:

• chr3-37190967-G-A
• rs13098279
• ENST00000702636.1:n.198-13708G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-37190967-G-A
• chr3-37190967-G-C

Variant summary

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

The ENST00000702636.1(ENSG00000290046):​n.198-13708G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,096 control chromosomes in the GnomAD database, including 4,354 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 0.22 (4354 hom., cov: 31)
• Consequence: ENSG00000290046 ENST00000702636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.15
• Publications: 9 publications found

Genes affected

ENSG00000290046 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377642	XR_002959625.2	n.208-13708G>A		intron_variant	Intron 1 of 3
LOC105377642	XR_007095869.1	n.111-13625G>A		intron_variant	Intron 1 of 2
LOC105377642	XR_007095870.1	n.208-13708G>A		intron_variant	Intron 1 of 3
LOC105377642	XR_007095871.1	n.111-13708G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290046	ENST00000702636.1	n.198-13708G>A		intron_variant	Intron 1 of 3
ENSG00000290046	ENST00000737037.1	n.109+14481G>A		intron_variant	Intron 1 of 2
ENSG00000290046	ENST00000737038.1	n.108-13708G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34046 AN: 151978 Hom.: 4356 Cov.: 31

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.224 AC: 34062 AN: 152096 Hom.: 4354 Cov.: 31 AF XY: 0.229 AC XY: 17059 AN XY: 74358

African (AFR) AF: 0.172 AC: 7149 AN: 41508

American (AMR) AF: 0.267 AC: 4074 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1037 AN: 3466

East Asian (EAS) AF: 0.553 AC: 2849 AN: 5152

South Asian (SAS) AF: 0.387 AC: 1869 AN: 4828

European-Finnish (FIN) AF: 0.212 AC: 2246 AN: 10578

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14080 AN: 67970

Other (OTH) AF: 0.249 AC: 524 AN: 2108

Alfa AF: 0.216 Hom.: 1578

Bravo AF: 0.228

Asia WGS AF: 0.442 AC: 1535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.7
DANN	Benign	0.47
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs13098279; hg19: chr3-37232458;