19-10631231-A-G

Variant names:

• chr19-10631231-A-G
• rs12972963
• NM_020428.4:c.331-44A>G

Variant summary

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

The NM_020428.4(SLC44A2):​c.331-44A>G 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 1,606,624 control chromosomes in the GnomAD database, including 492,213 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 (48582 hom., cov: 29)
  • Exomes 𝑓: 0.78 (443631 hom.)
• Consequence: SLC44A2 NM_020428.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.37

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC44A2	NM_020428.4	c.331-44A>G		intron_variant	Intron 5 of 21	ENST00000335757.10	NP_065161.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC44A2	ENST00000335757.10	c.331-44A>G		intron_variant	Intron 5 of 21	1	NM_020428.4	ENSP00000336888.4

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121199 AN: 151586 Hom.: 48555 Cov.: 29

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.795

GnomAD3 exomes AF: 0.793 AC: 199130 AN: 251258 Hom.: 79335 AF XY: 0.786 AC XY: 106737 AN XY: 135804

Gnomad AFR exome AF: 0.834

Gnomad AMR exome AF: 0.877

Gnomad ASJ exome AF: 0.755

Gnomad EAS exome AF: 0.689

Gnomad SAS exome AF: 0.759

Gnomad FIN exome AF: 0.825

Gnomad NFE exome AF: 0.785

Gnomad OTH exome AF: 0.773

GnomAD4 exome AF: 0.780 AC: 1134808 AN: 1454920 Hom.: 443631 Cov.: 32 AF XY: 0.779 AC XY: 564049 AN XY: 724204

Gnomad4 AFR exome AF: 0.834

Gnomad4 AMR exome AF: 0.872

Gnomad4 ASJ exome AF: 0.756

Gnomad4 EAS exome AF: 0.664

Gnomad4 SAS exome AF: 0.760

Gnomad4 FIN exome AF: 0.824

Gnomad4 NFE exome AF: 0.780

Gnomad4 OTH exome AF: 0.774

GnomAD4 genome AF: 0.799 AC: 121276 AN: 151704 Hom.: 48582 Cov.: 29 AF XY: 0.799 AC XY: 59243 AN XY: 74106

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.771

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.815

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.792

Alfa AF: 0.791 Hom.: 9799

Bravo AF: 0.799

Asia WGS AF: 0.763 AC: 2655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.12
DANN	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs12972963; hg19: chr19-10741907; COSMIC: COSV59836867; COSMIC: COSV59836867;