15-84972394-C-T

Position:

• chr15-84972394-C-T

Variant summary

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

The NM_001321722.2(SLC28A1):​c.1875-3111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,158 control chromosomes in the GnomAD database, including 30,514 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 0.63 (30514 hom., cov: 34)
• Consequence: SLC28A1 NM_001321722.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250

Genes affected

SLC28A1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC28A1	NM_001321721.2	c.*43-3111C>T		intron_variant			NP_001308650.1
SLC28A1	NM_001321722.2	c.1875-3111C>T		intron_variant			NP_001308651.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95528 AN: 152040 Hom.: 30484 Cov.: 34

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.628 AC: 95603 AN: 152158 Hom.: 30514 Cov.: 34 AF XY: 0.633 AC XY: 47084 AN XY: 74394

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.612

Alfa AF: 0.646 Hom.: 25090

Bravo AF: 0.621

Asia WGS AF: 0.672 AC: 2338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1109065; hg19: chr15-85515625;