4-187048175-A-G

Variant names:

• chr4-187048175-A-G
• rs6814129
• ENST00000651047.1:n.437-9751A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651047.1(ENSG00000250971):​n.437-9751A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 151,926 control chromosomes in the GnomAD database, including 25,751 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 0.58 (25751 hom., cov: 31)
• Consequence: ENSG00000250971 ENST00000651047.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175

Genes affected

ENSG00000250971 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723906	XR_002959826.2	n.394-9751A>G		intron_variant	Intron 2 of 3
LOC102723906	XR_007058501.1	n.394-9751A>G		intron_variant	Intron 2 of 2
LOC102723906	XR_007058502.1	n.394-9751A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250971	ENST00000651047.1	n.437-9751A>G		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87468 AN: 151808 Hom.: 25728 Cov.: 31

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.576 AC: 87551 AN: 151926 Hom.: 25751 Cov.: 31 AF XY: 0.569 AC XY: 42238 AN XY: 74212

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.571

Alfa AF: 0.557 Hom.: 48750

Bravo AF: 0.592

Asia WGS AF: 0.528 AC: 1835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6814129; hg19: chr4-187969329;