4-110306660-G-A

Variant names:

• chr4-110306660-G-A
• rs13148252
• ENST00000833186.1:n.255-43556G>A

Variant summary

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

The ENST00000833186.1(ENSG00000308313):​n.255-43556G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,140 control chromosomes in the GnomAD database, including 4,716 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 0.22 (4716 hom., cov: 33)
• Consequence: ENSG00000308313 ENST00000833186.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 6 publications found

Genes affected

ENSG00000308313 (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 (AMR) allele frequency at 95% confidence interval = 0.373 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
ENSG00000308313	ENST00000833186.1	n.255-43556G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34134 AN: 152022 Hom.: 4712 Cov.: 33

Gnomad AFR AF: 0.0821

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.224 AC: 34142 AN: 152140 Hom.: 4716 Cov.: 33 AF XY: 0.225 AC XY: 16738 AN XY: 74382

African (AFR) AF: 0.0820 AC: 3403 AN: 41524

American (AMR) AF: 0.382 AC: 5829 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 771 AN: 3466

East Asian (EAS) AF: 0.274 AC: 1418 AN: 5184

South Asian (SAS) AF: 0.175 AC: 843 AN: 4816

European-Finnish (FIN) AF: 0.217 AC: 2289 AN: 10564

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18816 AN: 67992

Other (OTH) AF: 0.236 AC: 499 AN: 2116

Alfa AF: 0.192 Hom.: 1975

Bravo AF: 0.235

Asia WGS AF: 0.215 AC: 745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.73
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs13148252; hg19: chr4-111227816;