16-24887651-C-A

Variant names:

• chr16-24887651-C-A
• rs274068
• NM_001352248.3:c.665-3218C>A

Variant summary

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

The NM_001352248.3(SLC5A11):​c.665-3218C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 151,984 control chromosomes in the GnomAD database, including 41,555 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 0.74 (41555 hom., cov: 32)
• Consequence: SLC5A11 NM_001352248.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 11 publications found

Genes affected

SLC5A11 (HGNC:23091): (solute carrier family 5 member 11) Cotransporters, such as SLC5A11, represent a major class of proteins that make use of ion gradients to drive active transport for the cellular accumulation of nutrients, neurotransmitters, osmolytes, and ions Roll et al. (2002) [PubMed 12039040].[supplied by OMIM, Mar 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC5A11	NM_001352248.3	c.665-3218C>A		intron_variant	Intron 9 of 16	ENST00000424767.7	NP_001339177.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC5A11	ENST00000424767.7	c.665-3218C>A		intron_variant	Intron 9 of 16	2	NM_001352248.3	ENSP00000416782.3

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112166 AN: 151866 Hom.: 41510 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.739 AC: 112277 AN: 151984 Hom.: 41555 Cov.: 32 AF XY: 0.738 AC XY: 54768 AN XY: 74256

African (AFR) AF: 0.747 AC: 30976 AN: 41468

American (AMR) AF: 0.781 AC: 11925 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2285 AN: 3472

East Asian (EAS) AF: 0.757 AC: 3919 AN: 5176

South Asian (SAS) AF: 0.716 AC: 3453 AN: 4820

European-Finnish (FIN) AF: 0.671 AC: 7064 AN: 10530

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.739 AC: 50183 AN: 67940

Other (OTH) AF: 0.738 AC: 1558 AN: 2110

Alfa AF: 0.739 Hom.: 147681

Bravo AF: 0.750

Asia WGS AF: 0.712 AC: 2452 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.62
PhyloP100		0.23
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: rs274068; hg19: chr16-24898972;