2-175424591-G-A

Position:

• chr2-175424591-G-A

Variant summary

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

The ENST00000438963.2(ENSG00000229066):​n.248-17857G>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 0.229 in 152,056 control chromosomes in the GnomAD database, including 4,512 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 0.23 (4512 hom., cov: 32)
• Consequence: ENST00000438963.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.53 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
	ENST00000438963.2	n.248-17857G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000444567.1	n.449-30017G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000653625.1	n.337-17857G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34717 AN: 151938 Hom.: 4512 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.229 AC: 34749 AN: 152056 Hom.: 4512 Cov.: 32 AF XY: 0.231 AC XY: 17196 AN XY: 74308

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.243

Alfa AF: 0.193 Hom.: 5986

Bravo AF: 0.242

Asia WGS AF: 0.403 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2461751; hg19: chr2-176289319;