rs17071722

chr6-110472889-C-T

Variant summary

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

The NM_033125.4(SLC22A16):c.53+3633G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,168 control chromosomes in the GnomAD database, including 1,365 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 0.12 (1365 hom., cov: 32)
• Consequence: SLC22A16 NM_033125.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

Genes affected

SLC22A16 (HGNC:20302): (solute carrier family 22 member 16) This gene encodes a member of the organic zwitterion transporter protein family which transports carnitine. The encoded protein has also been shown to transport anticancer drugs like bleomycin (PMID: 20037140) successful treatment has been correlated with the level of activity of this transporter in tumor cells. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A16	NM_033125.4	c.53+3633G>A		intron_variant		ENST00000368919.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A16	ENST00000368919.8	c.53+3633G>A		intron_variant		1	NM_033125.4	P2

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17981 AN: 152050 Hom.: 1365 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0946

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0752

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.118 AC: 18000 AN: 152168 Hom.: 1365 Cov.: 32 AF XY: 0.121 AC XY: 8974 AN XY: 74392

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0946

Gnomad4 NFE AF: 0.0752

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0925 Hom.: 293

Bravo AF: 0.122

Asia WGS AF: 0.163 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.2
Dann	Benign	0.64

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: rs17071722; hg19: chr6-110794092;