dbSNP rs10202029: SLC40A1:c.-103+344G>A (chr2-189581558-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000427419.5(SLC40A1):c.-103+344G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0864 in 152,396 control chromosomes in the GnomAD database, including 1,119 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 0.086 ( 1118 hom., cov: 31)

Exomes 𝑓: 0.032 ( 1 hom. )

Consequence

SLC40A1
ENST00000427419.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00800

Variant links:

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]

SLC40A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
SLC40A1	ENST00000427419.5 link	c.-103+344G>A	intron_variant	Intron 1 of 2	1	ENSP00000392730.1	Q4PNE6
SLC40A1	ENST00000440626.1 link	c.-64-1034G>A	intron_variant	Intron 1 of 2	1	ENSP00000396134.1	Q4PNE6
SLC40A1	ENST00000427241.5 link	c.-102-996G>A	intron_variant	Intron 2 of 7	5	ENSP00000390005.1	E7ES28
SLC40A1	ENST00000455320.5 link	c.-103+150G>A	intron_variant	Intron 1 of 3	3	ENSP00000413549.1	E7EQF8

Frequencies

GnomAD3 genomes

AF:

0.0863

AC:

13119

AN:

152026

Hom.:

1116

Cov.:

show subpopulations

Gnomad AFR

AF:

0.216

Gnomad AMI

AF:

0.0965

Gnomad AMR

AF:

0.0522

Gnomad ASJ

AF:

0.0404

Gnomad EAS

AF:

0.0248

Gnomad SAS

AF:

0.0838

Gnomad FIN

AF:

0.0188

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0327

Gnomad OTH

AF:

0.0831

GnomAD4 exome

AF:

0.0317

AC:

AN:

252

Hom.:

AF XY:

0.0357

AC XY:

AN XY:

196

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 AMR exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0324

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0864

AC:

13152

AN:

152144

Hom.:

1118

Cov.:

AF XY:

0.0850

AC XY:

6325

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.216

Gnomad4 AMR

AF:

0.0521

Gnomad4 ASJ

AF:

0.0404

Gnomad4 EAS

AF:

0.0247

Gnomad4 SAS

AF:

0.0845

Gnomad4 FIN

AF:

0.0188

Gnomad4 NFE

AF:

0.0326

Gnomad4 OTH

AF:

0.0818

Alfa

AF:

0.0544

Hom.:

115

Bravo

AF:

0.0953

Asia WGS

AF:

0.0630

AC:

218

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

7.1

DANN

Benign

0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over