ENST00000839902.1:n.452+46615C>T

Variant names:

• chr7-41782319-C-T
• rs12701937
• ENST00000839902.1:n.452+46615C>T

Variant summary

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

The ENST00000839902.1(ENSG00000309263):​n.452+46615C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,148 control chromosomes in the GnomAD database, including 8,859 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 0.30 (8859 hom., cov: 33)
• Consequence: ENSG00000309263 ENST00000839902.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 8 publications found

Genes affected

ENSG00000309263 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.41 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
ENSG00000309263	ENST00000839902.1	n.452+46615C>T		intron_variant	Intron 4 of 5
ENSG00000309263	ENST00000839903.1	n.245+46605C>T		intron_variant	Intron 3 of 3
ENSG00000309263	ENST00000839904.1	n.236+46615C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46332 AN: 152030 Hom.: 8866 Cov.: 33

Gnomad AFR AF: 0.0747

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.304 AC: 46315 AN: 152148 Hom.: 8859 Cov.: 33 AF XY: 0.307 AC XY: 22864 AN XY: 74378

African (AFR) AF: 0.0745 AC: 3097 AN: 41554

American (AMR) AF: 0.281 AC: 4291 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1645 AN: 3468

East Asian (EAS) AF: 0.326 AC: 1683 AN: 5158

South Asian (SAS) AF: 0.311 AC: 1501 AN: 4826

European-Finnish (FIN) AF: 0.448 AC: 4737 AN: 10580

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28177 AN: 67972

Other (OTH) AF: 0.318 AC: 672 AN: 2112

Alfa AF: 0.370 Hom.: 37133

Bravo AF: 0.280

Asia WGS AF: 0.291 AC: 1015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.58
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs12701937; hg19: chr7-41821917;