rs352038

Variant names:

• chr4-74052981-G-A
• rs352038
• ENST00000716529.1:n.312-1749G>A

Variant summary

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

The ENST00000716529.1(ENSG00000287037):​n.312-1749G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.944 in 152,234 control chromosomes in the GnomAD database, including 68,146 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 0.94 (68146 hom., cov: 33)
• Consequence: ENSG00000287037 ENST00000716529.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 3 publications found

Genes affected

ENSG00000287037 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.981 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
ENSG00000287037	ENST00000716529.1	n.312-1749G>A		intron_variant	Intron 2 of 5
ENSG00000287037	ENST00000716530.1	n.218-1749G>A		intron_variant	Intron 1 of 4
ENSG00000287037	ENST00000769988.1	n.335-1749G>A		intron_variant	Intron 3 of 4
ENSG00000287037	ENST00000769989.1	n.274-1749G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.944 AC: 143669 AN: 152116 Hom.: 68097 Cov.: 33

Gnomad AFR AF: 0.865

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.942

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.954

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

GnomAD4 genome AF: 0.944 AC: 143774 AN: 152234 Hom.: 68146 Cov.: 33 AF XY: 0.945 AC XY: 70322 AN XY: 74440

African (AFR) AF: 0.865 AC: 35895 AN: 41514

American (AMR) AF: 0.962 AC: 14709 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3415 AN: 3472

East Asian (EAS) AF: 0.831 AC: 4295 AN: 5166

South Asian (SAS) AF: 0.942 AC: 4550 AN: 4828

European-Finnish (FIN) AF: 0.995 AC: 10570 AN: 10622

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67118 AN: 68018

Other (OTH) AF: 0.954 AC: 2019 AN: 2116

Alfa AF: 0.975 Hom.: 85360

Bravo AF: 0.939

Asia WGS AF: 0.880 AC: 3061 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.43
DANN	Benign	0.63
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs352038; hg19: chr4-74918698;