rs4440020

Variant names:

• chr2-136232757-G-A
• rs4440020
• ENST00000624070.1:n.2005G>A

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000279024 ENST00000624070.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 3 publications found

Genes affected

ENSG00000279024 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000279024	ENST00000624070.1	n.2005G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 4 AN: 4

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.482 AC: 19987 AN: 41462

American (AMR) AF: 0.728 AC: 11129 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2606 AN: 3468

East Asian (EAS) AF: 0.585 AC: 3027 AN: 5172

South Asian (SAS) AF: 0.715 AC: 3442 AN: 4816

European-Finnish (FIN) AF: 0.870 AC: 9219 AN: 10602

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.878 AC: 59703 AN: 68024

Other (OTH) AF: 0.733 AC: 1547 AN: 2110

Alfa AF: 0.828 Hom.: 88902

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4440020; hg19: chr2-136990327;