rs4672503

Variant names:

• chr2-62322149-C-T
• rs4672503
• ENST00000687402.3:n.199+25703C>T

Variant summary

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

The ENST00000687402.3(ENSG00000228541):​n.199+25703C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,034 control chromosomes in the GnomAD database, including 8,577 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 0.33 (8577 hom., cov: 32)
• Consequence: ENSG00000228541 ENST00000687402.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 7 publications found

Genes affected

ENSG00000228541 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687402.3. 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
	ENSG00000228541	ENST00000687402.3		n.199+25703C>T		intron	N/A
	ENSG00000228541	ENST00000687773.2		n.199+25703C>T		intron	N/A
	ENSG00000228541	ENST00000688476.3		n.202-23765C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49428 AN: 151916 Hom.: 8584 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.325 AC: 49432 AN: 152034 Hom.: 8577 Cov.: 32 AF XY: 0.320 AC XY: 23811 AN XY: 74302

African (AFR) AF: 0.435 AC: 18007 AN: 41430

American (AMR) AF: 0.304 AC: 4651 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1185 AN: 3470

East Asian (EAS) AF: 0.429 AC: 2218 AN: 5176

South Asian (SAS) AF: 0.271 AC: 1307 AN: 4818

European-Finnish (FIN) AF: 0.234 AC: 2468 AN: 10550

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18574 AN: 67984

Other (OTH) AF: 0.326 AC: 689 AN: 2114

Alfa AF: 0.295 Hom.: 11617

Bravo AF: 0.340

Asia WGS AF: 0.348 AC: 1207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.1
DANN	Benign	0.83
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4672503;

hg19: chr2-62549284;