rs200514917

Variant names:

• chr20-62656690-C-G
• NM_016354.4:c.236C>G

Your query was ambiguous. Multiple possible variants found:

• chr20-62656690-C-G
• chr20-62656690-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_016354.4(SLCO4A1):​c.236C>G​(p.Ser79Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S79L) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 34)
• Consequence: SLCO4A1 NM_016354.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.90

Genes affected

SLCO4A1 (HGNC:10953): (solute carrier organic anion transporter family member 4A1) Predicted to enable sodium-independent organic anion transmembrane transporter activity and thyroid hormone transmembrane transporter activity. Predicted to be involved in sodium-independent organic anion transport. Predicted to be located in plasma membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO4A1	NM_016354.4	c.236C>G	p.Ser79Trp	missense_variant	Exon 2 of 12	ENST00000217159.6	NP_057438.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO4A1	ENST00000217159.6	c.236C>G	p.Ser79Trp	missense_variant	Exon 2 of 12	1	NM_016354.4	ENSP00000217159.1
SLCO4A1	ENST00000370507.5	c.236C>G	p.Ser79Trp	missense_variant	Exon 1 of 11	1		ENSP00000359538.1
SLCO4A1	ENST00000497209.5	n.236C>G		non_coding_transcript_exon_variant	Exon 2 of 10	1		ENSP00000434245.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Benign	-0.38
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Benign	0.29	T;T
Eigen	Benign	-0.029
Eigen_PC	Benign	-0.20
FATHMM_MKL	Benign	0.39	N
LIST_S2	Benign	0.83	T;.
M_CAP	Benign	0.031	D
MetaRNN	Uncertain	0.58	D;D
MetaSVM	Benign	-0.78	T
MutationAssessor	Benign	1.6	L;L
PrimateAI	Benign	0.40	T
PROVEAN	Uncertain	-4.2	D;D
REVEL	Benign	0.18
Sift	Uncertain	0.0010	D;D
Sift4G	Uncertain	0.0030	D;D
Polyphen		0.99	D;D
Vest4		0.45
MutPred		0.51		Loss of sheet (P = 0.0043);Loss of sheet (P = 0.0043);
MVP		0.75
MPC		0.92
ClinPred		0.98	D
GERP RS		3.8
Varity_R		0.27
gMVP		0.71

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-61288042;