rs4972990

Variant names:

• chr2-231414300-T-C
• rs4972990
• ENST00000827927.1:n.753T>C

Variant summary

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

The ENST00000827927.1(ENSG00000307696):​n.753T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,096 control chromosomes in the GnomAD database, including 10,667 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 0.37 (10667 hom., cov: 32)
• Consequence: ENSG00000307696 ENST00000827927.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14
• Publications: 4 publications found

Genes affected

ENSG00000307696 (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 (EAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827927.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307696	ENST00000827927.1		n.753T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000307696	ENST00000827928.1		n.656T>C		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000307696	ENST00000827929.1		n.980T>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56626 AN: 151978 Hom.: 10668 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.372 AC: 56647 AN: 152096 Hom.: 10667 Cov.: 32 AF XY: 0.372 AC XY: 27692 AN XY: 74378

African (AFR) AF: 0.334 AC: 13843 AN: 41468

American (AMR) AF: 0.341 AC: 5212 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1474 AN: 3470

East Asian (EAS) AF: 0.432 AC: 2232 AN: 5172

South Asian (SAS) AF: 0.378 AC: 1825 AN: 4826

European-Finnish (FIN) AF: 0.418 AC: 4422 AN: 10586

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26369 AN: 67960

Other (OTH) AF: 0.379 AC: 801 AN: 2116

Alfa AF: 0.380 Hom.: 4018

Bravo AF: 0.367

Asia WGS AF: 0.403 AC: 1405 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	1.2
DANN	Benign	0.31
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs4972990; hg19: chr2-232279011;