4-59157264-A-G

Variant names:

• chr4-59157264-A-G
• rs371989
• ENST00000512546.1:n.53+4378A>G

Variant summary

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

The ENST00000512546.1(ENSG00000249111):​n.53+4378A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 151,332 control chromosomes in the GnomAD database, including 6,567 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 0.28 (6567 hom., cov: 31)
• Consequence: ENSG00000249111 ENST00000512546.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 0 publications found

Genes affected

ENSG00000249111 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512546.1. 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
	ENSG00000249111	ENST00000512546.1	TSL:3	n.53+4378A>G		intron	N/A
	ENSG00000286097	ENST00000651732.1		n.241-4684T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42512 AN: 151218 Hom.: 6563 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.281 AC: 42520 AN: 151332 Hom.: 6567 Cov.: 31 AF XY: 0.281 AC XY: 20785 AN XY: 73906

African (AFR) AF: 0.143 AC: 5918 AN: 41412

American (AMR) AF: 0.373 AC: 5654 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1068 AN: 3462

East Asian (EAS) AF: 0.388 AC: 1984 AN: 5110

South Asian (SAS) AF: 0.274 AC: 1321 AN: 4814

European-Finnish (FIN) AF: 0.304 AC: 3165 AN: 10396

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22478 AN: 67662

Other (OTH) AF: 0.288 AC: 606 AN: 2104

Alfa AF: 0.176 Hom.: 381

Bravo AF: 0.285

Asia WGS AF: 0.273 AC: 942 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.3
DANN	Benign	0.66
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs371989; hg19: chr4-60022982;