rs1372788

Variant names:

• chr4-77481225-C-A
• rs1372788
• ENST00000513871.1:n.122+12940G>T

Your query was ambiguous. Multiple possible variants found:

• chr4-77481225-C-A
• chr4-77481225-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000513871.1(ENSG00000249036):​n.122+12940G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,636 control chromosomes in the GnomAD database, including 18,377 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 0.46 (18377 hom., cov: 31)
• Consequence: ENSG00000249036 ENST00000513871.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950

Genes affected

ENSG00000249036 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 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
ENSG00000249036	ENST00000513871.1	n.122+12940G>T		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69866 AN: 151518 Hom.: 18376 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.461 AC: 69868 AN: 151636 Hom.: 18377 Cov.: 31 AF XY: 0.459 AC XY: 34002 AN XY: 74060

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.497

Alfa AF: 0.432 Hom.: 1950

Bravo AF: 0.453

Asia WGS AF: 0.440 AC: 1530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1372788; hg19: chr4-78402379;