chr4-126444174-G-A

Position:

• chr4-126444174-G-A

Variant summary

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

The ENST00000661809.1(ENSG00000286251):​n.515-9233C>T 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 0.489 in 151,834 control chromosomes in the GnomAD database, including 21,099 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 0.49 (21099 hom., cov: 32)
• Consequence: ENST00000661809.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498

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 (NFE) allele frequency at 95% confidence interval = 0.648 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.515-9233C>T		intron_variant, non_coding_transcript_variant
	ENST00000651327.1	n.369-9233C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74267 AN: 151716 Hom.: 21093 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.489 AC: 74273 AN: 151834 Hom.: 21099 Cov.: 32 AF XY: 0.483 AC XY: 35843 AN XY: 74164

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.515

Alfa AF: 0.618 Hom.: 60862

Bravo AF: 0.480

Asia WGS AF: 0.417 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.75
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4833346; hg19: chr4-127365329;