ENST00000807137.1:n.59-1340G>A

Variant names:

• chr1-52593434-G-A
• rs835337
• ENST00000807137.1:n.59-1340G>A

Variant summary

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

The ENST00000807137.1(ENSG00000272371):​n.59-1340G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,152 control chromosomes in the GnomAD database, including 4,060 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 0.22 (4060 hom., cov: 32)
• Consequence: ENSG00000272371 ENST00000807137.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.969
• Publications: 14 publications found

Genes affected

ENSG00000272371 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.271 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
ENSG00000272371	ENST00000807137.1	n.59-1340G>A		intron_variant	Intron 1 of 2
ENSG00000272371	ENST00000807138.1	n.51-5315G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33988 AN: 152034 Hom.: 4054 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.224 AC: 34021 AN: 152152 Hom.: 4060 Cov.: 32 AF XY: 0.222 AC XY: 16517 AN XY: 74372

African (AFR) AF: 0.140 AC: 5816 AN: 41492

American (AMR) AF: 0.211 AC: 3222 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 888 AN: 3470

East Asian (EAS) AF: 0.203 AC: 1053 AN: 5182

South Asian (SAS) AF: 0.193 AC: 931 AN: 4824

European-Finnish (FIN) AF: 0.240 AC: 2541 AN: 10584

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.274 AC: 18622 AN: 68014

Other (OTH) AF: 0.236 AC: 499 AN: 2112

Alfa AF: 0.258 Hom.: 22331

Bravo AF: 0.221

Asia WGS AF: 0.163 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.72
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs835337; hg19: chr1-53059106;