rs1374951

Variant names:

• chr4-132986297-C-A
• rs1374951
• ENST00000511916.2:n.251-489G>T

Variant summary

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

The ENST00000511916.2(ENSG00000249513):​n.251-489G>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 152,152 control chromosomes in the GnomAD database, including 195 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 (195 hom., cov: 32)
• Consequence: ENSG00000249513 ENST00000511916.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0932 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
ENSG00000249513	ENST00000511916.2	n.251-489G>T		intron_variant	Intron 1 of 2	3
ENSG00000249513	ENST00000740310.1	n.147-686G>T		intron_variant	Intron 1 of 2
ENSG00000249513	ENST00000740311.1	n.129-689G>T		intron_variant	Intron 1 of 2
ENSG00000249513	ENST00000740312.1	n.255-686G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0332 AC: 5048 AN: 152034 Hom.: 195 Cov.: 32

Gnomad AFR AF: 0.0955

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0169

Gnomad ASJ AF: 0.0257

Gnomad EAS AF: 0.0261

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.00189

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00699

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: 5063 AN: 152152 Hom.: 195 Cov.: 32 AF XY: 0.0314 AC XY: 2338 AN XY: 74390

African (AFR) AF: 0.0957 AC: 3973 AN: 41506

American (AMR) AF: 0.0167 AC: 256 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0257 AC: 89 AN: 3466

East Asian (EAS) AF: 0.0261 AC: 135 AN: 5168

South Asian (SAS) AF: 0.00995 AC: 48 AN: 4826

European-Finnish (FIN) AF: 0.00189 AC: 20 AN: 10596

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00699 AC: 475 AN: 67984

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

Alfa AF: 0.0281 Hom.: 26

Bravo AF: 0.0376

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.049
DANN	Benign	0.29
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1374951; hg19: chr4-133907452;