rs4625554

Variant names:

• chr12-4307138-A-G
• rs4625554
• ENST00000674624.1:n.720+18148A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000674624.1(ENSG00000285901):​n.720+18148A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,148 control chromosomes in the GnomAD database, including 7,669 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 0.31 (7669 hom., cov: 32)
• Consequence: ENSG00000285901 ENST00000674624.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

ENSG00000285901 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285901	ENST00000674624.1	n.720+18148A>G		intron_variant	Intron 4 of 9			ENSP00000501898.1
ENSG00000285901	ENST00000648100.1	n.720+18148A>G		intron_variant	Intron 4 of 11			ENSP00000497536.1

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46688 AN: 152028 Hom.: 7652 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.307 AC: 46758 AN: 152148 Hom.: 7669 Cov.: 32 AF XY: 0.313 AC XY: 23279 AN XY: 74366

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.311

Alfa AF: 0.308 Hom.: 728

Bravo AF: 0.313

Asia WGS AF: 0.337 AC: 1173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.029
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4625554; hg19: chr12-4416304;