20-62659008-C-T

Position:

• chr20-62659008-C-T

Variant summary

Our verdict is Benign. Variant got -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

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 Benign. Variant got -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/exons	MANE	UniProt
SLCO4A1	NM_016354.4	c.887+241C>T		intron_variant		ENST00000217159.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO4A1	ENST00000217159.6	c.887+241C>T		intron_variant		1	NM_016354.4	P1
SLCO4A1	ENST00000370507.5	c.887+241C>T		intron_variant		1		P1
SLCO4A1	ENST00000497209.5	c.887+241C>T		intron_variant, NMD_transcript_variant		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

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.0498

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.192

Alfa AF: 0.173 Hom.: 2961

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
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

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: rs872626; hg19: chr20-61290360;