2-175802375-G-T

Variant names:

• chr2-175802375-G-T
• rs1992788
• ENST00000685522.2:n.464-30236G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000685522.2(ENSG00000289349):​n.464-30236G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,014 control chromosomes in the GnomAD database, including 4,566 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 0.24 (4566 hom., cov: 32)
• Consequence: ENSG00000289349 ENST00000685522.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 1 publications found

Genes affected

ENSG00000289349 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685522.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289349	ENST00000685522.2		n.464-30236G>T		intron	N/A
	ENSG00000289349	ENST00000692740.2		n.326-30236G>T		intron	N/A
	ENSG00000289349	ENST00000840653.1		n.272-30236G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36293 AN: 151896 Hom.: 4563 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.239 AC: 36334 AN: 152014 Hom.: 4566 Cov.: 32 AF XY: 0.243 AC XY: 18066 AN XY: 74286

African (AFR) AF: 0.188 AC: 7810 AN: 41490

American (AMR) AF: 0.200 AC: 3054 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1021 AN: 3468

East Asian (EAS) AF: 0.186 AC: 962 AN: 5162

South Asian (SAS) AF: 0.367 AC: 1769 AN: 4820

European-Finnish (FIN) AF: 0.307 AC: 3225 AN: 10520

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17750 AN: 67960

Other (OTH) AF: 0.265 AC: 561 AN: 2116

Alfa AF: 0.264 Hom.: 2973

Bravo AF: 0.229

Asia WGS AF: 0.237 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.55
PhyloP100		-0.032

Splicing

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

Other links and lift over

dbSNP: rs1992788; hg19: chr2-176667103;