rs7851395

Variant names:

• chr9-113240184-A-G
• rs7851395
• NM_001859.4:c.-35-15930A>G

Your query was ambiguous. Multiple possible variants found:

• chr9-113240184-A-G
• chr9-113240184-A-T

Variant summary

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

The NM_001859.4(SLC31A1):​c.-35-15930A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,934 control chromosomes in the GnomAD database, including 17,161 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 0.47 (17161 hom., cov: 32)
• Consequence: SLC31A1 NM_001859.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 15 publications found

Genes affected

SLC31A1 (HGNC:11016): (solute carrier family 31 member 1) The protein encoded by this gene is a high-affinity copper transporter found in the cell membrane. The encoded protein functions as a homotrimer to effect the uptake of dietary copper. [provided by RefSeq, Aug 2011]

SLC31A1 Gene-Disease associations (from GenCC):

• neurodegeneration and seizures due to copper transport defect

  Inheritance: AR, Unknown Classification: MODERATE, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)

LOC107987119 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001859.4. 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
	SLC31A1	NM_001859.4	MANE Select	c.-35-15930A>G		intron	N/A	NP_001850.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC31A1	ENST00000374212.5	TSL:1 MANE Select	c.-35-15930A>G		intron	N/A	ENSP00000363329.4

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71454 AN: 151816 Hom.: 17145 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.471 AC: 71524 AN: 151934 Hom.: 17161 Cov.: 32 AF XY: 0.475 AC XY: 35262 AN XY: 74272

African (AFR) AF: 0.533 AC: 22071 AN: 41400

American (AMR) AF: 0.416 AC: 6355 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1829 AN: 3470

East Asian (EAS) AF: 0.482 AC: 2488 AN: 5162

South Asian (SAS) AF: 0.588 AC: 2835 AN: 4820

European-Finnish (FIN) AF: 0.474 AC: 5002 AN: 10544

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29421 AN: 67952

Other (OTH) AF: 0.450 AC: 948 AN: 2108

Alfa AF: 0.454 Hom.: 22820

Bravo AF: 0.471

Asia WGS AF: 0.565 AC: 1958 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.64
PhyloP100		-0.16
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: rs7851395; hg19: chr9-116002464;