4-151987017-G-A

Variant names:

• chr4-151987017-G-A
• rs360932
• ENST00000652265.1:n.1354+3555C>T

Variant summary

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

The ENST00000652265.1(ENSG00000286066):​n.1354+3555C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 152,012 control chromosomes in the GnomAD database, including 24,436 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 0.55 (24436 hom., cov: 32)
• Consequence: ENSG00000286066 ENST00000652265.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576
• Publications: 9 publications found

Genes affected

ENSG00000286066 (HGNC:):

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 = 0.658 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
ENSG00000286066	ENST00000652265.1	n.1354+3555C>T		intron_variant	Intron 1 of 1
ENSG00000286066	ENST00000731965.1	n.210+4705C>T		intron_variant	Intron 1 of 1
ENSG00000286066	ENST00000731966.1	n.374+3737C>T		intron_variant	Intron 2 of 2
ENSG00000286066	ENST00000731967.1	n.1343+3555C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84251 AN: 151894 Hom.: 24417 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.555 AC: 84305 AN: 152012 Hom.: 24436 Cov.: 32 AF XY: 0.541 AC XY: 40216 AN XY: 74294

African (AFR) AF: 0.461 AC: 19102 AN: 41446

American (AMR) AF: 0.545 AC: 8316 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1913 AN: 3472

East Asian (EAS) AF: 0.132 AC: 685 AN: 5178

South Asian (SAS) AF: 0.415 AC: 1999 AN: 4820

European-Finnish (FIN) AF: 0.504 AC: 5326 AN: 10574

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45035 AN: 67956

Other (OTH) AF: 0.588 AC: 1236 AN: 2102

Alfa AF: 0.615 Hom.: 55295

Bravo AF: 0.556

Asia WGS AF: 0.335 AC: 1164 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.18
DANN	Benign	0.17
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs360932; hg19: chr4-152908169;