2-17805416-G-T

Variant names:

• chr2-17805416-G-T
• rs300152
• ENST00000750479.1:n.454-462C>A

Variant summary

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

The ENST00000750479.1(ENSG00000297720):​n.454-462C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 151,840 control chromosomes in the GnomAD database, including 7,488 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 0.27 (7488 hom., cov: 32)
• Consequence: ENSG00000297720 ENST00000750479.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112
• Publications: 5 publications found

Genes affected

ENSG00000297720 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750479.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297720	ENST00000750479.1		n.454-462C>A		intron	N/A
	ENSG00000297720	ENST00000750480.1		n.637-462C>A		intron	N/A
	ENSG00000297720	ENST00000750481.1		n.596-462C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41138 AN: 151722 Hom.: 7464 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.271 AC: 41207 AN: 151840 Hom.: 7488 Cov.: 32 AF XY: 0.283 AC XY: 20978 AN XY: 74194

African (AFR) AF: 0.239 AC: 9895 AN: 41374

American (AMR) AF: 0.458 AC: 6988 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 627 AN: 3470

East Asian (EAS) AF: 0.945 AC: 4885 AN: 5172

South Asian (SAS) AF: 0.413 AC: 1987 AN: 4806

European-Finnish (FIN) AF: 0.243 AC: 2559 AN: 10538

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13593 AN: 67924

Other (OTH) AF: 0.283 AC: 597 AN: 2106

Alfa AF: 0.231 Hom.: 654

Bravo AF: 0.289

Asia WGS AF: 0.661 AC: 2294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.10
DANN	Benign	0.53
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs300152; hg19: chr2-17986683;