rs2151499

Variant names:

• chr13-22655014-G-A
• rs2151499
• ENST00000815334.1:n.440-3254C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-22655014-G-A
• chr13-22655014-G-T

Variant summary

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

The ENST00000815334.1(ENSG00000306102):​n.440-3254C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,200 control chromosomes in the GnomAD database, including 1,922 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 0.14 (1922 hom., cov: 33)
• Consequence: ENSG00000306102 ENST00000815334.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 1 publications found

Genes affected

ENSG00000306102 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000815334.1. 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
	ENSG00000306102	ENST00000815334.1		n.440-3254C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21954 AN: 152084 Hom.: 1921 Cov.: 33

Gnomad AFR AF: 0.0617

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.144 AC: 21957 AN: 152200 Hom.: 1922 Cov.: 33 AF XY: 0.150 AC XY: 11191 AN XY: 74400

African (AFR) AF: 0.0615 AC: 2555 AN: 41550

American (AMR) AF: 0.150 AC: 2296 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 461 AN: 3468

East Asian (EAS) AF: 0.266 AC: 1373 AN: 5166

South Asian (SAS) AF: 0.122 AC: 586 AN: 4816

European-Finnish (FIN) AF: 0.294 AC: 3115 AN: 10586

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11097 AN: 68008

Other (OTH) AF: 0.142 AC: 300 AN: 2114

Alfa AF: 0.142 Hom.: 267

Bravo AF: 0.127

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.47
PhyloP100		-0.035

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: rs2151499;

hg19: chr13-23229153;