rs12359361

Variant names:

• chr10-8488303-C-T
• rs12359361

Variant summary

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

The variant allele was found at a frequency of 0.0745 in 152,172 control chromosomes in the GnomAD database, including 485 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 0.074 (485 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0946 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

Frequencies

GnomAD3 genomes AF: 0.0744 AC: 11311 AN: 152054 Hom.: 484 Cov.: 33

Gnomad AFR AF: 0.0969

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0698

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.0827

Gnomad FIN AF: 0.0363

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0695

Gnomad OTH AF: 0.0909

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

GnomAD4 genome AF: 0.0745 AC: 11330 AN: 152172 Hom.: 485 Cov.: 33 AF XY: 0.0726 AC XY: 5403 AN XY: 74398

African (AFR) AF: 0.0971 AC: 4031 AN: 41510

American (AMR) AF: 0.0697 AC: 1066 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 360 AN: 3468

East Asian (EAS) AF: 0.0259 AC: 134 AN: 5178

South Asian (SAS) AF: 0.0822 AC: 396 AN: 4820

European-Finnish (FIN) AF: 0.0363 AC: 385 AN: 10602

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0696 AC: 4729 AN: 67992

Other (OTH) AF: 0.0894 AC: 188 AN: 2102

Alfa AF: 0.0739 Hom.: 308

Bravo AF: 0.0784

Asia WGS AF: 0.0540 AC: 190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.41
PhyloP100		-0.045

Splicing

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

Other links and lift over

dbSNP: rs12359361; hg19: chr10-8530266;