2-175827903-G-T

Position:

• chr2-175827903-G-T

Variant summary

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

The ENST00000685522.1(ENSG00000289349):​n.394-4708G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,956 control chromosomes in the GnomAD database, including 20,920 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 0.51 (20920 hom., cov: 32)
• Consequence: ENSG00000289349 ENST00000685522.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479

Genes affected

ENSG00000289349 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985962	XR_007087312.1	n.149+10987C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289349	ENST00000685522.1	n.394-4708G>T		intron_variant
ENSG00000289349	ENST00000692740.1	n.251-4708G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77991 AN: 151838 Hom.: 20895 Cov.: 32

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.514 AC: 78067 AN: 151956 Hom.: 20920 Cov.: 32 AF XY: 0.508 AC XY: 37686 AN XY: 74246

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.482

Alfa AF: 0.464 Hom.: 12085

Bravo AF: 0.528

Asia WGS AF: 0.539 AC: 1877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.56
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1374431; hg19: chr2-176692631;