chr5-159313842-A-G

Variant names:

• chr5-159313842-A-G
• rs3181224
• ENST00000521472.6:n.289+2428A>G

Variant summary

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

The ENST00000521472.6(ENSG00000249738):​n.289+2428A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,282 control chromosomes in the GnomAD database, including 842 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 0.10 (842 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000521472.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543
• Publications: 29 publications found

Genes affected

ENSG00000249738 (HGNC:58156):

LOC105377683 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.135 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521472.6. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249738	ENST00000521472.6	TSL:3	n.289+2428A>G		intron	N/A
	ENSG00000249738	ENST00000764992.1		n.380+2428A>G		intron	N/A
	ENSG00000249738	ENST00000765003.1		n.387+2428A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15444 AN: 152162 Hom.: 838 Cov.: 32

Gnomad AFR AF: 0.0851

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0404

Gnomad SAS AF: 0.0642

Gnomad FIN AF: 0.0712

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.101 AC: 15456 AN: 152282 Hom.: 842 Cov.: 32 AF XY: 0.0988 AC XY: 7355 AN XY: 74454

African (AFR) AF: 0.0850 AC: 3532 AN: 41558

American (AMR) AF: 0.139 AC: 2134 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 637 AN: 3472

East Asian (EAS) AF: 0.0405 AC: 210 AN: 5190

South Asian (SAS) AF: 0.0640 AC: 309 AN: 4826

European-Finnish (FIN) AF: 0.0712 AC: 755 AN: 10600

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7486 AN: 68014

Other (OTH) AF: 0.118 AC: 249 AN: 2114

Alfa AF: 0.113 Hom.: 3230

Bravo AF: 0.109

Asia WGS AF: 0.0610 AC: 211 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.43
DANN	Benign	0.22
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs3181224; hg19: chr5-158740850;