2-239783349-C-T

Variant names:

• chr2-239783349-C-T
• rs12614692
• ENST00000407524.1:n.195+2924C>T

Variant summary

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

The ENST00000407524.1(ENSG00000220256):​n.195+2924C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,198 control chromosomes in the GnomAD database, including 1,167 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 0.12 (1167 hom., cov: 33)
• Consequence: ENSG00000220256 ENST00000407524.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.405
• Publications: 6 publications found

Genes affected

ENSG00000220256 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC150935	NR_037808.1	n.195+2924C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000220256	ENST00000407524.1	n.195+2924C>T		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18358 AN: 152078 Hom.: 1168 Cov.: 33

Gnomad AFR AF: 0.0857

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0940

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.121 AC: 18358 AN: 152198 Hom.: 1167 Cov.: 33 AF XY: 0.124 AC XY: 9197 AN XY: 74404

African (AFR) AF: 0.0857 AC: 3557 AN: 41526

American (AMR) AF: 0.0939 AC: 1437 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0818 AC: 284 AN: 3470

East Asian (EAS) AF: 0.150 AC: 776 AN: 5168

South Asian (SAS) AF: 0.175 AC: 845 AN: 4818

European-Finnish (FIN) AF: 0.163 AC: 1728 AN: 10590

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9374 AN: 68004

Other (OTH) AF: 0.117 AC: 248 AN: 2112

Alfa AF: 0.130 Hom.: 4167

Bravo AF: 0.113

Asia WGS AF: 0.136 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.40
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs12614692; hg19: chr2-240705043;