rs352054

Variant names:

• chr4-74015033-G-A
• rs352054
• ENST00000716529.1:n.311+15671G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-74015033-G-A
• chr4-74015033-G-C

Variant summary

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

The ENST00000716529.1(ENSG00000287037):​n.311+15671G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.927 in 152,208 control chromosomes in the GnomAD database, including 65,502 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 0.93 (65502 hom., cov: 31)
• Consequence: ENSG00000287037 ENST00000716529.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 4 publications found

Genes affected

ENSG00000287037 (HGNC:58815):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.957 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.311+15671G>A		intron_variant	Intron 2 of 5
ENSG00000287037	ENST00000769988.1	n.278+15671G>A		intron_variant	Intron 2 of 4
ENSG00000287037	ENST00000769990.1	n.743+15671G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.927 AC: 140945 AN: 152090 Hom.: 65461 Cov.: 31

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.925

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

GnomAD4 genome AF: 0.927 AC: 141042 AN: 152208 Hom.: 65502 Cov.: 31 AF XY: 0.925 AC XY: 68838 AN XY: 74422

African (AFR) AF: 0.857 AC: 35551 AN: 41504

American (AMR) AF: 0.937 AC: 14318 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3123 AN: 3472

East Asian (EAS) AF: 0.948 AC: 4896 AN: 5164

South Asian (SAS) AF: 0.912 AC: 4401 AN: 4828

European-Finnish (FIN) AF: 0.962 AC: 10203 AN: 10610

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.963 AC: 65530 AN: 68024

Other (OTH) AF: 0.924 AC: 1954 AN: 2114

Alfa AF: 0.942 Hom.: 26088

Bravo AF: 0.922

Asia WGS AF: 0.895 AC: 3112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.50
PhyloP100		0.080

Splicing

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

Other links and lift over

dbSNP: rs352054; hg19: chr4-74880750;