rs4440020

chr2-136232757-G-A

Variant summary

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

The ENST00000624070.1(ENSG00000279024):n.2005G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,146 control chromosomes in the GnomAD database, including 43,355 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 0.73 (43353 hom., cov: 32)
  • Exomes 𝑓: 1.0 (2 hom.)
• Consequence: ENST00000624070.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.872 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
	ENST00000624070.1	n.2005G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111665 AN: 152024 Hom.: 43361 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.738

GnomAD4 exome AF: 1.00 AC: 4 AN: 4 Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.734 AC: 111695 AN: 152142 Hom.: 43353 Cov.: 32 AF XY: 0.732 AC XY: 54468 AN XY: 74382

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.751

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.733

Alfa AF: 0.841 Hom.: 71518

Bravo AF: 0.712

Asia WGS AF: 0.596 AC: 2077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.15
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4440020; hg19: chr2-136990327;