chr2-44298871-G-A

Variant names:

• chr2-44298871-G-A
• rs2165421
• NM_000341.4:c.892-1100G>A

Variant summary

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

The NM_000341.4(SLC3A1):​c.892-1100G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,816 control chromosomes in the GnomAD database, including 28,341 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 0.61 (28341 hom., cov: 30)
• Consequence: SLC3A1 NM_000341.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

Genes affected

SLC3A1 (HGNC:11025): (solute carrier family 3 member 1) This gene encodes a type II membrane glycoprotein which is one of the components of the renal amino acid transporter which transports neutral and basic amino acids in the renal tubule and intestinal tract. Mutations and deletions in this gene are associated with cystinuria. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

ENSG00000285542 (HGNC:):

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 = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC3A1	NM_000341.4	c.892-1100G>A		intron_variant	Intron 4 of 9	ENST00000260649.11	NP_000332.2
SLC3A1	XM_011533047.4	c.892-1100G>A		intron_variant	Intron 4 of 9		XP_011531349.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC3A1	ENST00000260649.11	c.892-1100G>A		intron_variant	Intron 4 of 9	1	NM_000341.4	ENSP00000260649.6
ENSG00000285542	ENST00000649044.1	n.*903-1100G>A		intron_variant	Intron 9 of 14			ENSP00000497083.1

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91923 AN: 151696 Hom.: 28345 Cov.: 30

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.606 AC: 91949 AN: 151816 Hom.: 28341 Cov.: 30 AF XY: 0.598 AC XY: 44389 AN XY: 74188

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.607

Alfa AF: 0.647 Hom.: 13594

Bravo AF: 0.600

Asia WGS AF: 0.478 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.34

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: rs2165421; hg19: chr2-44526010;