4-143319320-A-G

Variant names:

• chr4-143319320-A-G
• rs300905
• ENST00000512715.1:n.45-9959A>G

Variant summary

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

The ENST00000512715.1(ENSG00000250969):​n.45-9959A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,720 control chromosomes in the GnomAD database, including 18,084 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 0.47 (18084 hom., cov: 31)
• Consequence: ENSG00000250969 ENST00000512715.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 5 publications found

Genes affected

ENSG00000250969 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 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
ENSG00000250969	ENST00000512715.1	n.45-9959A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71712 AN: 151602 Hom.: 18084 Cov.: 31

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.473 AC: 71746 AN: 151720 Hom.: 18084 Cov.: 31 AF XY: 0.480 AC XY: 35570 AN XY: 74156

African (AFR) AF: 0.297 AC: 12267 AN: 41316

American (AMR) AF: 0.538 AC: 8200 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1662 AN: 3468

East Asian (EAS) AF: 0.741 AC: 3812 AN: 5144

South Asian (SAS) AF: 0.410 AC: 1968 AN: 4802

European-Finnish (FIN) AF: 0.623 AC: 6554 AN: 10514

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

European-Non Finnish (NFE) AF: 0.524 AC: 35604 AN: 67914

Other (OTH) AF: 0.477 AC: 1004 AN: 2106

Alfa AF: 0.508 Hom.: 85654

Bravo AF: 0.462

Asia WGS AF: 0.516 AC: 1794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.6
DANN	Benign	0.89
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs300905; hg19: chr4-144240473;