rs13398147

Variant names:

• chr2-221895559-C-T
• rs13398147
• ENST00000755241.1:n.87-12657C>T

Variant summary

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

The ENST00000755241.1(ENSG00000298385):​n.87-12657C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,088 control chromosomes in the GnomAD database, including 3,073 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 0.20 (3073 hom., cov: 32)
• Consequence: ENSG00000298385 ENST00000755241.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 12 publications found

Genes affected

ENSG00000298385 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

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
ENSG00000298385	ENST00000755241.1	n.87-12657C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29891 AN: 151970 Hom.: 3074 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.197 AC: 29893 AN: 152088 Hom.: 3073 Cov.: 32 AF XY: 0.197 AC XY: 14683 AN XY: 74352

African (AFR) AF: 0.137 AC: 5682 AN: 41508

American (AMR) AF: 0.188 AC: 2878 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 772 AN: 3468

East Asian (EAS) AF: 0.223 AC: 1153 AN: 5162

South Asian (SAS) AF: 0.286 AC: 1379 AN: 4818

European-Finnish (FIN) AF: 0.251 AC: 2658 AN: 10574

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.216 AC: 14659 AN: 67968

Other (OTH) AF: 0.190 AC: 401 AN: 2108

Alfa AF: 0.211 Hom.: 1912

Bravo AF: 0.183

Asia WGS AF: 0.236 AC: 819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.59
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs13398147; hg19: chr2-222760279;