rs1372788

Positions:

• 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, non coding transcript 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: ENST00000513871.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000513871.1	n.122+12940G>T		intron_variant, non_coding_transcript_variant		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;