chr3-38302467-G-A

Position:

• chr3-38302467-G-A

Variant summary

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

The NM_001320033.2(SLC22A14):​c.1-3560G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0691 in 151,572 control chromosomes in the GnomAD database, including 382 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 0.069 (382 hom., cov: 31)
• Consequence: SLC22A14 NM_001320033.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249

Genes affected

SLC22A14 (HGNC:8495): (solute carrier family 22 member 14) This gene encodes a member of the organic-cation transporter family. It is located in a gene cluster with another member of the family, organic cation transporter like 3. The encoded protein is a transmembrane protein which is thought to transport small molecules and since this protein is conserved among several species, it is suggested to have a fundamental role in mammalian systems. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A14	NM_001320033.2	c.1-3560G>A		intron_variant		ENST00000448498.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A14	ENST00000448498.6	c.1-3560G>A		intron_variant		1	NM_001320033.2	P1
SLC22A14	ENST00000466887.5	c.-119-3837G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0691 AC: 10468 AN: 151458 Hom.: 381 Cov.: 31

Gnomad AFR AF: 0.0665

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.0675

Gnomad ASJ AF: 0.0873

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0233

Gnomad FIN AF: 0.0413

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.0721

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

GnomAD4 genome AF: 0.0691 AC: 10472 AN: 151572 Hom.: 382 Cov.: 31 AF XY: 0.0662 AC XY: 4897 AN XY: 73992

Gnomad4 AFR AF: 0.0664

Gnomad4 AMR AF: 0.0674

Gnomad4 ASJ AF: 0.0873

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0235

Gnomad4 FIN AF: 0.0413

Gnomad4 NFE AF: 0.0836

Gnomad4 OTH AF: 0.0714

Alfa AF: 0.0713 Hom.: 52

Bravo AF: 0.0717

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.2
DANN	Benign	0.43

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: rs151632; hg19: chr3-38343958;