4-126659277-A-G

Variant names:

• chr4-126659277-A-G
• rs386871
• ENST00000661809.1:n.148+38988T>C

Variant summary

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

The ENST00000661809.1(ENSG00000286251):​n.148+38988T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.866 in 152,042 control chromosomes in the GnomAD database, including 57,215 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 0.87 (57215 hom., cov: 31)
• Consequence: ENSG00000286251 ENST00000661809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612

Genes affected

ENSG00000286251 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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
ENSG00000286251	ENST00000661809.1	n.148+38988T>C		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131585 AN: 151924 Hom.: 57169 Cov.: 31

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.950

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.866 AC: 131690 AN: 152042 Hom.: 57215 Cov.: 31 AF XY: 0.873 AC XY: 64906 AN XY: 74326

Gnomad4 AFR AF: 0.888

Gnomad4 AMR AF: 0.883

Gnomad4 ASJ AF: 0.893

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.950

Gnomad4 FIN AF: 0.905

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.855

Alfa AF: 0.836 Hom.: 90017

Bravo AF: 0.865

Asia WGS AF: 0.962 AC: 3343 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs386871; hg19: chr4-127580432;