15-65053624-G-T

Variant names:

• chr15-65053624-G-T
• rs1046482
• NM_016563.4:c.*1275C>A

Variant summary

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

The NM_016563.4(RASL12):​c.*1275C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 989,792 control chromosomes in the GnomAD database, including 376,260 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 0.88 (59083 hom., cov: 32)
  • Exomes 𝑓: 0.87 (317177 hom.)
• Consequence: RASL12 NM_016563.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741

Genes affected

RASL12 (HGNC:30289): (RAS like family 12) Predicted to enable GDP binding activity; GTP binding activity; and GTPase activity. Predicted to be involved in signal transduction. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC51B (HGNC:29956): (SLC51 subunit beta) Predicted to enable protein heterodimerization activity and transmembrane transporter activity. Involved in bile acid secretion. Located in basolateral plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RASL12	NM_016563.4	c.*1275C>A		3_prime_UTR_variant	Exon 5 of 5	ENST00000220062.9	NP_057647.1
SLC51B	NM_178859.4	c.*460G>T		downstream_gene_variant		ENST00000334287.3	NP_849190.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RASL12	ENST00000220062	c.*1275C>A		3_prime_UTR_variant	Exon 5 of 5	1	NM_016563.4	ENSP00000220062.4
SLC51B	ENST00000334287.3	c.*460G>T		downstream_gene_variant		2	NM_178859.4	ENSP00000335292.2

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133915 AN: 152122 Hom.: 59030 Cov.: 32

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.878

GnomAD4 exome AF: 0.870 AC: 728879 AN: 837552 Hom.: 317177 Cov.: 45 AF XY: 0.870 AC XY: 336887 AN XY: 387176

Gnomad4 AFR exome AF: 0.890

Gnomad4 AMR exome AF: 0.867

Gnomad4 ASJ exome AF: 0.894

Gnomad4 EAS exome AF: 0.990

Gnomad4 SAS exome AF: 0.915

Gnomad4 FIN exome AF: 0.891

Gnomad4 NFE exome AF: 0.868

Gnomad4 OTH exome AF: 0.878

GnomAD4 genome AF: 0.880 AC: 134026 AN: 152240 Hom.: 59083 Cov.: 32 AF XY: 0.881 AC XY: 65610 AN XY: 74454

Gnomad4 AFR AF: 0.895

Gnomad4 AMR AF: 0.862

Gnomad4 ASJ AF: 0.888

Gnomad4 EAS AF: 0.985

Gnomad4 SAS AF: 0.916

Gnomad4 FIN AF: 0.881

Gnomad4 NFE AF: 0.864

Gnomad4 OTH AF: 0.879

Alfa AF: 0.867 Hom.: 47077

Bravo AF: 0.882

Asia WGS AF: 0.920 AC: 3201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.36
DANN	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1046482; hg19: chr15-65345962;