ENST00000435996.1:n.242+58469G>A

Variant names:

• chr7-136235882-G-A
• rs1426483
• ENST00000435996.1:n.242+58469G>A

Variant summary

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

The ENST00000435996.1(ENSG00000232053):​n.242+58469G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,076 control chromosomes in the GnomAD database, including 35,726 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 0.68 (35726 hom., cov: 32)
• Consequence: ENSG00000232053 ENST00000435996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474
• Publications: 2 publications found

Genes affected

ENSG00000232053 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375523	NR_187952.1	n.113-6268G>A		intron_variant	Intron 1 of 1
LOC105375523	NR_187953.1	n.315-6268G>A		intron_variant	Intron 3 of 3
LOC105375523	NR_187954.1	n.421-6268G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232053	ENST00000435996.1	n.242+58469G>A		intron_variant	Intron 2 of 3	3
ENSG00000232053	ENST00000445293.6	n.393-6268G>A		intron_variant	Intron 3 of 6	5
ENSG00000232053	ENST00000657456.1	n.287-6268G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103732 AN: 151958 Hom.: 35686 Cov.: 32

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.683 AC: 103828 AN: 152076 Hom.: 35726 Cov.: 32 AF XY: 0.682 AC XY: 50665 AN XY: 74322

African (AFR) AF: 0.700 AC: 29044 AN: 41480

American (AMR) AF: 0.725 AC: 11072 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2540 AN: 3472

East Asian (EAS) AF: 0.869 AC: 4493 AN: 5168

South Asian (SAS) AF: 0.744 AC: 3586 AN: 4822

European-Finnish (FIN) AF: 0.551 AC: 5817 AN: 10554

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44955 AN: 67998

Other (OTH) AF: 0.707 AC: 1495 AN: 2114

Alfa AF: 0.676 Hom.: 56643

Bravo AF: 0.700

Asia WGS AF: 0.825 AC: 2869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.61
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1426483; hg19: chr7-135920630;