4-126659277-A-G

Position:

• chr4-126659277-A-G

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, non coding transcript 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: ENST00000661809.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661809.1	n.148+38988T>C		intron_variant, non_coding_transcript_variant

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;