2-239806946-G-A

Position:

• chr2-239806946-G-A

Variant summary

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

The ENST00000650712.1(ENSG00000220256):​n.1915-5233G>A 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 0.124 in 152,296 control chromosomes in the GnomAD database, including 1,383 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 0.12 (1383 hom., cov: 33)
• Consequence: ENST00000650712.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.155 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
	ENST00000650712.1	n.1915-5233G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18905 AN: 152178 Hom.: 1382 Cov.: 33

Gnomad AFR AF: 0.0729

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0484

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.124 AC: 18921 AN: 152296 Hom.: 1383 Cov.: 33 AF XY: 0.122 AC XY: 9080 AN XY: 74460

Gnomad4 AFR AF: 0.0729

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.0485

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.141

Alfa AF: 0.149 Hom.: 1343

Bravo AF: 0.121

Asia WGS AF: 0.0870 AC: 301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11695034; hg19: chr2-240728640;