3-196233354-A-G

Variant names:

• chr3-196233354-A-G
• rs9343
• NM_152672.6:c.*155A>G

Variant summary

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

The NM_152672.6(SLC51A):​c.*155A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 831,946 control chromosomes in the GnomAD database, including 108,085 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 0.50 (19609 hom., cov: 33)
  • Exomes 𝑓: 0.50 (88476 hom.)
• Consequence: SLC51A NM_152672.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

Genes affected

SLC51A (HGNC:29955): (solute carrier family 51 member A) Predicted to enable protein heterodimerization activity; protein homodimerization activity; and transmembrane transporter activity. Involved in bile acid secretion. Located in basolateral plasma membrane. Implicated in progressive familial intrahepatic cholestasis. [provided by Alliance of Genome Resources, Apr 2022]

PCYT1A (HGNC:8754): (phosphate cytidylyltransferase 1A, choline) This gene belongs to the cytidylyltransferase family and is involved in the regulation of phosphatidylcholine biosynthesis. Mutations in this gene are associated with spondylometaphyseal dysplasia with cone-rod dystrophy. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2015]

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 = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC51A	NM_152672.6	c.*155A>G		3_prime_UTR_variant	Exon 9 of 9	ENST00000296327.10	NP_689885.4
SLC51A	XM_047447662.1	c.*155A>G		3_prime_UTR_variant	Exon 8 of 8		XP_047303618.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC51A	ENST00000296327.10	c.*155A>G		3_prime_UTR_variant	Exon 9 of 9	1	NM_152672.6	ENSP00000296327.5

Frequencies

GnomAD3 genomes AF: 0.500 AC: 76102 AN: 152052 Hom.: 19578 Cov.: 33

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.487

GnomAD4 exome AF: 0.499 AC: 339050 AN: 679776 Hom.: 88476 Cov.: 9 AF XY: 0.499 AC XY: 174355 AN XY: 349352

Gnomad4 AFR exome AF: 0.506

Gnomad4 AMR exome AF: 0.550

Gnomad4 ASJ exome AF: 0.419

Gnomad4 EAS exome AF: 0.883

Gnomad4 SAS exome AF: 0.539

Gnomad4 FIN exome AF: 0.430

Gnomad4 NFE exome AF: 0.473

Gnomad4 OTH exome AF: 0.490

GnomAD4 genome AF: 0.501 AC: 76181 AN: 152170 Hom.: 19609 Cov.: 33 AF XY: 0.503 AC XY: 37433 AN XY: 74408

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.489

Alfa AF: 0.464 Hom.: 5544

Bravo AF: 0.512

Asia WGS AF: 0.686 AC: 2383 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	2.8
DANN	Benign	0.61
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs9343; hg19: chr3-195960225; COSMIC: COSV53057145; COSMIC: COSV53057145;