rs1360573

Variant names:

• chr10-36596993-A-G
• rs1360573
• ENST00000790386.1:n.195-1801T>C

Variant summary

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

The ENST00000790386.1(ENSG00000302912):​n.195-1801T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,102 control chromosomes in the GnomAD database, including 4,593 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 0.24 (4593 hom., cov: 32)
• Consequence: ENSG00000302912 ENST00000790386.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 7 publications found

Genes affected

ENSG00000302912 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302912	ENST00000790386.1	n.195-1801T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36672 AN: 151984 Hom.: 4585 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.241 AC: 36711 AN: 152102 Hom.: 4593 Cov.: 32 AF XY: 0.236 AC XY: 17586 AN XY: 74366

African (AFR) AF: 0.276 AC: 11471 AN: 41490

American (AMR) AF: 0.165 AC: 2525 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1022 AN: 3468

East Asian (EAS) AF: 0.120 AC: 621 AN: 5168

South Asian (SAS) AF: 0.169 AC: 816 AN: 4824

European-Finnish (FIN) AF: 0.239 AC: 2528 AN: 10574

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.246 AC: 16755 AN: 67986

Other (OTH) AF: 0.254 AC: 536 AN: 2110

Alfa AF: 0.245 Hom.: 8138

Bravo AF: 0.241

Asia WGS AF: 0.154 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.11
DANN	Benign	0.50
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1360573; hg19: chr10-36885921;