rs1123110

Variant names:

• chr2-189579473-G-A
• rs1123110
• NM_014585.6:c.111+340C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-189579473-G-A
• chr2-189579473-G-C

Variant summary

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

The NM_014585.6(SLC40A1):​c.111+340C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,994 control chromosomes in the GnomAD database, including 25,269 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 0.56 (25269 hom., cov: 32)
• Consequence: SLC40A1 NM_014585.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

SLC40A1 (HGNC:10909): (solute carrier family 40 member 1) The protein encoded by this gene is a cell membrane protein that may be involved in iron export from duodenal epithelial cells. Defects in this gene are a cause of hemochromatosis type 4 (HFE4). [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC40A1	NM_014585.6	c.111+340C>T		intron_variant	Intron 2 of 7	ENST00000261024.7	NP_055400.1
SLC40A1	XM_047444066.1	c.-145+340C>T		intron_variant	Intron 1 of 7		XP_047300022.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC40A1	ENST00000261024.7	c.111+340C>T		intron_variant	Intron 2 of 7	1	NM_014585.6	ENSP00000261024.3

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84988 AN: 151874 Hom.: 25263 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.559 AC: 85023 AN: 151994 Hom.: 25269 Cov.: 32 AF XY: 0.565 AC XY: 41952 AN XY: 74294

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.571

Alfa AF: 0.622 Hom.: 49358

Bravo AF: 0.554

Asia WGS AF: 0.646 AC: 2243 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.68
DANN	Benign	0.51

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: rs1123110; hg19: chr2-190444199;