rs11581062

Variant names:

• chr1-100941963-A-G
• rs11581062
• NM_133496.5:c.843-19865A>G

Variant summary

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

The NM_133496.5(SLC30A7):​c.843-19865A>G variant causes a intron change. The variant allele was found at a frequency of 0.276 in 271,428 control chromosomes in the GnomAD database, including 10,848 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 0.28 (6085 hom., cov: 32)
  • Exomes 𝑓: 0.27 (4763 hom.)
• Consequence: SLC30A7 NM_133496.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.20
• Publications: 55 publications found

Genes affected

SLC30A7 (HGNC:19306): (solute carrier family 30 member 7) Zinc functions as a cofactor for numerous enzymes, nuclear factors, and hormones and as an intra- and intercellular signal ion. Members of the zinc transporter (ZNT)/SLC30 subfamily of the cation diffusion facilitator family, such as SLC30A7, permit cellular efflux of zinc (Seve et al., 2004 [PubMed 15154973]).[supplied by OMIM, Mar 2008]

HNRNPA1P68 (HGNC:48798): (heterogeneous nuclear ribonucleoprotein A1 pseudogene 68)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC30A7	NM_133496.5	c.843-19865A>G		intron_variant	Intron 8 of 10	ENST00000357650.9	NP_598003.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC30A7	ENST00000357650.9	c.843-19865A>G		intron_variant	Intron 8 of 10	1	NM_133496.5	ENSP00000350278.4
SLC30A7	ENST00000370112.8	c.843-19865A>G		intron_variant	Intron 8 of 11	1		ENSP00000359130.4
HNRNPA1P68	ENST00000425806.2	n.33T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
SLC30A7	ENST00000850622.1	n.843-19865A>G		intron_variant	Intron 8 of 12			ENSP00000520907.1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42409 AN: 151998 Hom.: 6056 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.293

GnomAD4 exome AF: 0.272 AC: 32466 AN: 119312 Hom.: 4763 Cov.: 0 AF XY: 0.271 AC XY: 17262 AN XY: 63744

African (AFR) AF: 0.330 AC: 1097 AN: 3322

American (AMR) AF: 0.217 AC: 1526 AN: 7026

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1265 AN: 3318

East Asian (EAS) AF: 0.148 AC: 1002 AN: 6790

South Asian (SAS) AF: 0.205 AC: 3034 AN: 14798

European-Finnish (FIN) AF: 0.236 AC: 1075 AN: 4550

Middle Eastern (MID) AF: 0.284 AC: 159 AN: 560

European-Non Finnish (NFE) AF: 0.298 AC: 21430 AN: 72032

Other (OTH) AF: 0.272 AC: 1878 AN: 6916

GnomAD4 genome AF: 0.279 AC: 42477 AN: 152116 Hom.: 6085 Cov.: 32 AF XY: 0.273 AC XY: 20281 AN XY: 74346

African (AFR) AF: 0.313 AC: 12972 AN: 41458

American (AMR) AF: 0.240 AC: 3662 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1267 AN: 3468

East Asian (EAS) AF: 0.151 AC: 784 AN: 5186

South Asian (SAS) AF: 0.187 AC: 899 AN: 4818

European-Finnish (FIN) AF: 0.211 AC: 2234 AN: 10592

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19750 AN: 68000

Other (OTH) AF: 0.296 AC: 625 AN: 2114

Alfa AF: 0.288 Hom.: 29243

Bravo AF: 0.283

Asia WGS AF: 0.202 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	2.3
DANN	Benign	0.58
PhyloP100		5.2
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: rs11581062; hg19: chr1-101407519; COSMIC: COSV63017170;