20-62659008-C-T

Variant names:

• chr20-62659008-C-T
• rs872626
• NM_016354.4:c.887+241C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016354.4(SLCO4A1):​c.887+241C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,240 control chromosomes in the GnomAD database, including 2,936 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 0.19 (2936 hom., cov: 34)
• Consequence: SLCO4A1 NM_016354.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO4A1	NM_016354.4	c.887+241C>T		intron_variant	Intron 3 of 11	ENST00000217159.6	NP_057438.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO4A1	ENST00000217159.6	c.887+241C>T		intron_variant	Intron 3 of 11	1	NM_016354.4	ENSP00000217159.1
SLCO4A1	ENST00000370507.5	c.887+241C>T		intron_variant	Intron 2 of 10	1		ENSP00000359538.1
SLCO4A1	ENST00000497209.5	n.887+241C>T		intron_variant	Intron 3 of 9	1		ENSP00000434245.1

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29221 AN: 152122 Hom.: 2920 Cov.: 34

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.0497

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.193

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.192 AC: 29282 AN: 152240 Hom.: 2936 Cov.: 34 AF XY: 0.193 AC XY: 14344 AN XY: 74422

African (AFR) AF: 0.241 AC: 10013 AN: 41544

American (AMR) AF: 0.208 AC: 3189 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 918 AN: 3468

East Asian (EAS) AF: 0.0498 AC: 258 AN: 5182

South Asian (SAS) AF: 0.159 AC: 765 AN: 4826

European-Finnish (FIN) AF: 0.203 AC: 2150 AN: 10596

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11259 AN: 68004

Other (OTH) AF: 0.192 AC: 406 AN: 2116

Alfa AF: 0.175 Hom.: 3918

Bravo AF: 0.194

Asia WGS AF: 0.125 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.15
DANN	Benign	0.42
PhyloP100		-1.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs872626; hg19: chr20-61290360;