rs7519615

Positions:

• chr1-219873960-C-T

Variant summary

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

The ENST00000484239.5(SLC30A10):​n.575+10166G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.087 in 151,986 control chromosomes in the GnomAD database, including 1,443 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 0.087 (1443 hom., cov: 31)
• Consequence: SLC30A10 ENST00000484239.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

Genes affected

SLC30A10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372926	XR_001738474.1	n.173+10166G>A		intron_variant
LOC105372926	XR_001738475.1	n.173+10166G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC30A10	ENST00000484239.5	n.575+10166G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0870 AC: 13212 AN: 151868 Hom.: 1439 Cov.: 31

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.00982

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.0274

Gnomad FIN AF: 0.00359

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.00615

Gnomad OTH AF: 0.0736

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

GnomAD4 genome AF: 0.0870 AC: 13230 AN: 151986 Hom.: 1443 Cov.: 31 AF XY: 0.0873 AC XY: 6486 AN XY: 74282

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.00982

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.0270

Gnomad4 FIN AF: 0.00359

Gnomad4 NFE AF: 0.00615

Gnomad4 OTH AF: 0.0728

Alfa AF: 0.0362 Hom.: 243

Bravo AF: 0.107

Asia WGS AF: 0.118 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.2
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7519615; hg19: chr1-220047302;