rs1560711

Variant names:

• chr19-10631611-C-T
• rs1560711
• NM_020428.4:c.503-15C>T

Variant summary

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

The NM_020428.4(SLC44A2):​c.503-15C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 1,613,388 control chromosomes in the GnomAD database, including 494,889 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 0.80 (48879 hom., cov: 33)
  • Exomes 𝑓: 0.78 (446010 hom.)
• Consequence: SLC44A2 NM_020428.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 18 publications found

Genes affected

SLC44A2 (HGNC:17292): (solute carrier family 44 member 2 (CTL2 blood group)) Enables choline transmembrane transporter activity. Involved in choline transport and transmembrane transport. Located in mitochondrion and 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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020428.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC44A2	NM_020428.4	MANE Select	c.503-15C>T		intron	N/A	NP_065161.3
	SLC44A2	NM_001363611.2		c.503-15C>T		intron	N/A	NP_001350540.1
	SLC44A2	NM_001145056.2		c.497-15C>T		intron	N/A	NP_001138528.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC44A2	ENST00000335757.10	TSL:1 MANE Select	c.503-15C>T		intron	N/A	ENSP00000336888.4
	SLC44A2	ENST00000407327.8	TSL:1	c.497-15C>T		intron	N/A	ENSP00000385135.3
	SLC44A2	ENST00000588465.5	TSL:1	n.412-15C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121741 AN: 152032 Hom.: 48853 Cov.: 33

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.796

GnomAD2 exomes AF: 0.793 AC: 198074 AN: 249860 AF XY: 0.786

Gnomad AFR exome AF: 0.839

Gnomad AMR exome AF: 0.876

Gnomad ASJ exome AF: 0.754

Gnomad EAS exome AF: 0.687

Gnomad FIN exome AF: 0.824

Gnomad NFE exome AF: 0.784

Gnomad OTH exome AF: 0.774

GnomAD4 exome AF: 0.780 AC: 1140364 AN: 1461238 Hom.: 446010 Cov.: 80 AF XY: 0.779 AC XY: 566514 AN XY: 726898

African (AFR) AF: 0.839 AC: 28070 AN: 33476

American (AMR) AF: 0.872 AC: 38973 AN: 44676

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 19738 AN: 26132

East Asian (EAS) AF: 0.665 AC: 26400 AN: 39680

South Asian (SAS) AF: 0.763 AC: 65842 AN: 86238

European-Finnish (FIN) AF: 0.824 AC: 43733 AN: 53076

Middle Eastern (MID) AF: 0.695 AC: 4004 AN: 5764

European-Non Finnish (NFE) AF: 0.780 AC: 866880 AN: 1111812

Other (OTH) AF: 0.774 AC: 46724 AN: 60384

GnomAD4 genome AF: 0.801 AC: 121818 AN: 152150 Hom.: 48879 Cov.: 33 AF XY: 0.801 AC XY: 59562 AN XY: 74378

African (AFR) AF: 0.840 AC: 34897 AN: 41530

American (AMR) AF: 0.827 AC: 12630 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 2668 AN: 3468

East Asian (EAS) AF: 0.683 AC: 3524 AN: 5156

South Asian (SAS) AF: 0.773 AC: 3731 AN: 4826

European-Finnish (FIN) AF: 0.813 AC: 8625 AN: 10604

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

European-Non Finnish (NFE) AF: 0.783 AC: 53231 AN: 67980

Other (OTH) AF: 0.792 AC: 1672 AN: 2110

Alfa AF: 0.796 Hom.: 16545

Bravo AF: 0.801

Asia WGS AF: 0.761 AC: 2648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.8
DANN	Benign	0.61
PhyloP100		1.5
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: rs1560711; hg19: chr19-10742287; COSMIC: COSV59836886; COSMIC: COSV59836886;