rs6477998

Positions:

• chr9-113234969-C-A

Variant summary

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

The NM_001859.4(SLC31A1):​c.-36+13291C>A 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 151,822 control chromosomes in the GnomAD database, including 17,187 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 (17187 hom., cov: 32)
• Consequence: SLC31A1 NM_001859.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667

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]

LOC107987119 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC31A1	NM_001859.4	c.-36+13291C>A		intron_variant		ENST00000374212.5	NP_001850.1
LOC107987119	XR_007061736.1	n.7180G>T		non_coding_transcript_exon_variant	2/2
LOC107987119	XR_007061737.1	n.7055G>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC31A1	ENST00000374212.5	c.-36+13291C>A		intron_variant		1	NM_001859.4	ENSP00000363329.4

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71506 AN: 151704 Hom.: 17171 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.475

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: 71576 AN: 151822 Hom.: 17187 Cov.: 32 AF XY: 0.475 AC XY: 35263 AN XY: 74196

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.450

Alfa AF: 0.444 Hom.: 31283

Bravo AF: 0.471

Asia WGS AF: 0.566 AC: 1962 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.49
DANN	Benign	0.61

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: rs6477998; hg19: chr9-115997249; COSMIC: COSV65264737;