chr15-65051697-G-A

Position:

• chr15-65051697-G-A

Variant summary

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

The NM_178859.4(SLC51B):​c.188+92G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.882 in 1,190,930 control chromosomes in the GnomAD database, including 463,788 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 0.89 (60428 hom., cov: 29)
  • Exomes 𝑓: 0.88 (403360 hom.)
• Consequence: SLC51B NM_178859.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423

Genes affected

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]

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]

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 = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC51B	NM_178859.4	c.188+92G>A		intron_variant		ENST00000334287.3	NP_849190.2
RASL12	XM_017022296.2	c.*293C>T		3_prime_UTR_variant	5/5		XP_016877785.1
RASL12	XM_005254434.5	c.426-5953C>T		intron_variant			XP_005254491.1
SLC51B	XM_005254159.6	c.188+92G>A		intron_variant			XP_005254216.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC51B	ENST00000334287.3	c.188+92G>A		intron_variant		2	NM_178859.4	ENSP00000335292.2

Frequencies

GnomAD3 genomes AF: 0.891 AC: 135320 AN: 151902 Hom.: 60375 Cov.: 29

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.884

GnomAD4 exome AF: 0.881 AC: 915126 AN: 1038910 Hom.: 403360 AF XY: 0.882 AC XY: 468441 AN XY: 531210

Gnomad4 AFR exome AF: 0.924

Gnomad4 AMR exome AF: 0.878

Gnomad4 ASJ exome AF: 0.897

Gnomad4 EAS exome AF: 0.979

Gnomad4 SAS exome AF: 0.921

Gnomad4 FIN exome AF: 0.873

Gnomad4 NFE exome AF: 0.871

Gnomad4 OTH exome AF: 0.886

GnomAD4 genome AF: 0.891 AC: 135431 AN: 152020 Hom.: 60428 Cov.: 29 AF XY: 0.891 AC XY: 66230 AN XY: 74314

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.891

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.867

Gnomad4 OTH AF: 0.885

Alfa AF: 0.874 Hom.: 8028

Bravo AF: 0.894

Asia WGS AF: 0.925 AC: 3216 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	0.62
DANN	Benign	0.66

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: rs2946676; hg19: chr15-65344035;