rs3181226

Variant names:

• chr5-159313522-C-G
• rs3181226
• ENST00000521472.6:n.289+2108C>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+2108C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,086 control chromosomes in the GnomAD database, including 1,968 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 0.15 (1968 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000521472.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 11 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377683	XR_941138.3	n.401-1696C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249738	ENST00000521472.6	n.289+2108C>G		intron_variant	Intron 2 of 3	3
ENSG00000249738	ENST00000764992.1	n.380+2108C>G		intron_variant	Intron 2 of 4
ENSG00000249738	ENST00000765003.1	n.387+2108C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23124 AN: 151968 Hom.: 1964 Cov.: 32

Gnomad AFR AF: 0.0813

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.152 AC: 23138 AN: 152086 Hom.: 1968 Cov.: 32 AF XY: 0.154 AC XY: 11449 AN XY: 74342

African (AFR) AF: 0.0813 AC: 3374 AN: 41502

American (AMR) AF: 0.128 AC: 1955 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 736 AN: 3468

East Asian (EAS) AF: 0.172 AC: 885 AN: 5144

South Asian (SAS) AF: 0.120 AC: 578 AN: 4814

European-Finnish (FIN) AF: 0.248 AC: 2627 AN: 10580

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

European-Non Finnish (NFE) AF: 0.184 AC: 12481 AN: 67978

Other (OTH) AF: 0.167 AC: 351 AN: 2108

Alfa AF: 0.166 Hom.: 292

Bravo AF: 0.142

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.49
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs3181226; hg19: chr5-158740530;