ENST00000439694.6:n.655+2540A>G

Variant names:

• chr7-137029365-T-C
• rs324656
• ENST00000439694.6:n.655+2540A>G

Variant summary

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

The ENST00000439694.6(ENSG00000234352):​n.655+2540A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 151,828 control chromosomes in the GnomAD database, including 12,767 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 0.40 (12767 hom., cov: 32)
• Consequence: ENSG00000234352 ENST00000439694.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 0 publications found

Genes affected

ENSG00000234352 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC349160	NR_046103.1	n.341+3429A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234352	ENST00000439694.6	n.655+2540A>G		intron_variant	Intron 3 of 3	1
ENSG00000234352	ENST00000425981.2	n.341+3429A>G		intron_variant	Intron 2 of 3	2
ENSG00000234352	ENST00000586239.5	n.273+3429A>G		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.402 AC: 60919 AN: 151710 Hom.: 12748 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.402 AC: 60962 AN: 151828 Hom.: 12767 Cov.: 32 AF XY: 0.405 AC XY: 30048 AN XY: 74170

African (AFR) AF: 0.339 AC: 14019 AN: 41392

American (AMR) AF: 0.510 AC: 7771 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1357 AN: 3470

East Asian (EAS) AF: 0.643 AC: 3275 AN: 5090

South Asian (SAS) AF: 0.569 AC: 2743 AN: 4820

European-Finnish (FIN) AF: 0.353 AC: 3724 AN: 10546

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26763 AN: 67952

Other (OTH) AF: 0.398 AC: 839 AN: 2108

Alfa AF: 0.390 Hom.: 4368

Bravo AF: 0.408

Asia WGS AF: 0.587 AC: 2043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	10
DANN	Benign	0.86
PhyloP100		0.0040

Splicing

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

Other links and lift over

dbSNP: rs324656; hg19: chr7-136714112;