chr4-132986110-G-A

Variant names:

• chr4-132986110-G-A
• rs1374952
• ENST00000511916.2:n.251-302C>T

Variant summary

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

The ENST00000511916.2(ENSG00000249513):​n.251-302C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0333 in 152,044 control chromosomes in the GnomAD database, including 198 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 0.033 (198 hom., cov: 32)
• Consequence: ENSG00000249513 ENST00000511916.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61
• Publications: 0 publications found

Genes affected

ENSG00000249513 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0932 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511916.2. 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
	ENSG00000249513	ENST00000511916.2	TSL:3	n.251-302C>T		intron	N/A
	ENSG00000249513	ENST00000740310.1		n.147-499C>T		intron	N/A
	ENSG00000249513	ENST00000740311.1		n.129-502C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0332 AC: 5042 AN: 151944 Hom.: 198 Cov.: 32

Gnomad AFR AF: 0.0954

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0170

Gnomad ASJ AF: 0.0257

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.00189

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00697

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0333 AC: 5057 AN: 152044 Hom.: 198 Cov.: 32 AF XY: 0.0314 AC XY: 2337 AN XY: 74320

African (AFR) AF: 0.0956 AC: 3964 AN: 41446

American (AMR) AF: 0.0169 AC: 258 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0257 AC: 89 AN: 3468

East Asian (EAS) AF: 0.0264 AC: 137 AN: 5180

South Asian (SAS) AF: 0.00997 AC: 48 AN: 4816

European-Finnish (FIN) AF: 0.00189 AC: 20 AN: 10556

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.00697 AC: 474 AN: 67990

Other (OTH) AF: 0.0279 AC: 59 AN: 2114

Alfa AF: 0.00644 Hom.: 4

Bravo AF: 0.0377

Asia WGS AF: 0.0420 AC: 147 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.3
DANN	Benign	0.52
PhyloP100		1.6
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1374952; hg19: chr4-133907265;