8-69672988-G-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_030958.3(SLCO5A1):c.2428C>T(p.Leu810=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.002 in 1,614,070 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0015 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0021 (5 hom.)
• Consequence: SLCO5A1 NM_030958.3 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.13

Genes affected

SLCO5A1 (HGNC:19046): (solute carrier organic anion transporter family member 5A1) Predicted to enable sodium-independent organic anion transmembrane transporter activity. Predicted to be involved in sodium-independent organic anion transport. Located in intracellular membrane-bounded organelle and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BP6: Variant 8-69672988-G-A is Benign according to our data. Variant chr8-69672988-G-A is described in ClinVar as [Benign]. Clinvar id is 782750.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=2.13 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO5A1	NM_030958.3	c.2428C>T	p.Leu810=	synonymous_variant	10/10	ENST00000260126.9
SLCO5A1	NM_001146009.1	c.2263C>T	p.Leu755=	synonymous_variant	8/8
SLCO5A1	NM_001146008.2	c.*299C>T		3_prime_UTR_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO5A1	ENST00000260126.9	c.2428C>T	p.Leu810=	synonymous_variant	10/10	1	NM_030958.3	P1
SLCO5A1	ENST00000530307.1	c.2263C>T	p.Leu755=	synonymous_variant	8/8	1
SLCO5A1	ENST00000524945.5	c.*299C>T		3_prime_UTR_variant	8/8	2
SLCO5A1	ENST00000526750.1	c.*774C>T		3_prime_UTR_variant, NMD_transcript_variant	6/6	5

Frequencies

GnomAD3 genomes AF: 0.00148 AC: 225 AN: 152176 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000627

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000327

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.00132

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00259

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.00161 AC: 405 AN: 251362 Hom.: 1 AF XY: 0.00146 AC XY: 199 AN XY: 135852

Gnomad AFR exome AF: 0.000308

Gnomad AMR exome AF: 0.000260

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000719

Gnomad FIN exome AF: 0.00199

Gnomad NFE exome AF: 0.00281

Gnomad OTH exome AF: 0.00114

GnomAD4 exome AF: 0.00206 AC: 3008 AN: 1461894 Hom.: 5 Cov.: 31 AF XY: 0.00203 AC XY: 1475 AN XY: 727248

Gnomad4 AFR exome AF: 0.000239

Gnomad4 AMR exome AF: 0.000201

Gnomad4 ASJ exome AF: 0.0000383

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000672

Gnomad4 FIN exome AF: 0.00148

Gnomad4 NFE exome AF: 0.00250

Gnomad4 OTH exome AF: 0.00121

GnomAD4 genome AF: 0.00148 AC: 225 AN: 152176 Hom.: 0 Cov.: 33 AF XY: 0.00145 AC XY: 108 AN XY: 74332

Gnomad4 AFR AF: 0.000627

Gnomad4 AMR AF: 0.000327

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000621

Gnomad4 FIN AF: 0.00132

Gnomad4 NFE AF: 0.00259

Gnomad4 OTH AF: 0.000478

Alfa AF: 0.00180 Hom.: 0

Bravo AF: 0.00138

EpiCase AF: 0.00311

EpiControl AF: 0.00219

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 23, 2024

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
Cadd	Benign	3.8
Dann	Benign	0.69

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: rs150778647; hg19: chr8-70585223;