4-87975269-T-C

Variant names:

• chr4-87975269-T-C
• rs11730582
• ENST00000662475.1:n.901A>G

Variant summary

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

The ENST00000662475.1(ENSG00000286618):​n.901A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,224 control chromosomes in the GnomAD database, including 12,625 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 0.37 (12625 hom., cov: 33)
• Consequence: ENSG00000286618 ENST00000662475.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.56
• Publications: 112 publications found

Genes affected

ENSG00000286618 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.523 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
ENSG00000286618	ENST00000662475.1	n.901A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56993 AN: 152106 Hom.: 12625 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.374 AC: 56998 AN: 152224 Hom.: 12625 Cov.: 33 AF XY: 0.375 AC XY: 27888 AN XY: 74430

African (AFR) AF: 0.123 AC: 5101 AN: 41564

American (AMR) AF: 0.439 AC: 6701 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2004 AN: 3470

East Asian (EAS) AF: 0.341 AC: 1772 AN: 5190

South Asian (SAS) AF: 0.540 AC: 2608 AN: 4828

European-Finnish (FIN) AF: 0.414 AC: 4387 AN: 10592

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33060 AN: 67988

Other (OTH) AF: 0.409 AC: 863 AN: 2112

Alfa AF: 0.444 Hom.: 45117

Bravo AF: 0.365

Asia WGS AF: 0.414 AC: 1442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.13
DANN	Benign	0.44
PhyloP100		-3.6
PromoterAI		-0.0080	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11730582; hg19: chr4-88896421;