rs13006237

Variant names:

• chr2-123757465-G-A
• rs13006237
• ENST00000773411.1:n.629-19146C>T

Variant summary

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

The ENST00000773411.1(ENSG00000300686):​n.629-19146C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 151,834 control chromosomes in the GnomAD database, including 4,556 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 0.21 (4556 hom., cov: 32)
• Consequence: ENSG00000300686 ENST00000773411.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 5 publications found

Genes affected

ENSG00000300686 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773411.1. 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
	ENSG00000300686	ENST00000773411.1		n.629-19146C>T		intron	N/A
	ENSG00000300686	ENST00000773412.1		n.314-19146C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32565 AN: 151716 Hom.: 4555 Cov.: 32

Gnomad AFR AF: 0.0665

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0209

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.215 AC: 32572 AN: 151834 Hom.: 4556 Cov.: 32 AF XY: 0.210 AC XY: 15575 AN XY: 74188

African (AFR) AF: 0.0664 AC: 2751 AN: 41422

American (AMR) AF: 0.173 AC: 2646 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3470

East Asian (EAS) AF: 0.0207 AC: 107 AN: 5162

South Asian (SAS) AF: 0.158 AC: 763 AN: 4818

European-Finnish (FIN) AF: 0.307 AC: 3213 AN: 10462

Middle Eastern (MID) AF: 0.121 AC: 35 AN: 290

European-Non Finnish (NFE) AF: 0.320 AC: 21758 AN: 67928

Other (OTH) AF: 0.190 AC: 402 AN: 2112

Alfa AF: 0.269 Hom.: 9684

Bravo AF: 0.193

Asia WGS AF: 0.115 AC: 401 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.27
PhyloP100		-1.4

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: rs13006237;

hg19: chr2-124515041;