rs12504628

Variant names:

• chr4-144515172-T-C
• rs12504628
• ENST00000649263.1:n.328-99194A>G

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-99194A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 152,108 control chromosomes in the GnomAD database, including 9,719 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 (9719 hom., cov: 33)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.909
• Publications: 53 publications found

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649263.1. 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
	ENSG00000285713	ENST00000649263.1		n.328-99194A>G		intron	N/A	ENSP00000497507.1	A0A3B3ISY7
	ENSG00000285783	ENST00000650526.1		n.223-99194A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50490 AN: 151988 Hom.: 9707 Cov.: 33

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.332 AC: 50513 AN: 152108 Hom.: 9719 Cov.: 33 AF XY: 0.339 AC XY: 25193 AN XY: 74344

African (AFR) AF: 0.140 AC: 5797 AN: 41528

American (AMR) AF: 0.318 AC: 4862 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1115 AN: 3468

East Asian (EAS) AF: 0.306 AC: 1580 AN: 5170

South Asian (SAS) AF: 0.499 AC: 2406 AN: 4822

European-Finnish (FIN) AF: 0.538 AC: 5677 AN: 10552

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27940 AN: 67968

Other (OTH) AF: 0.317 AC: 668 AN: 2110

Alfa AF: 0.383 Hom.: 33787

Bravo AF: 0.300

Asia WGS AF: 0.365 AC: 1271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	11
DANN	Benign	0.90
PhyloP100		0.91

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: rs12504628;

hg19: chr4-145436324;