rs12218361

Positions:

• chr10-124381580-A-G
• chr10-124381580-A-T

Variant summary

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

The variant allele was found at a frequency of 0.126 in 152,070 control chromosomes in the GnomAD database, including 2,018 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 0.13 (2018 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19162 AN: 151952 Hom.: 2010 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0309

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0631

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.126 AC: 19201 AN: 152070 Hom.: 2018 Cov.: 32 AF XY: 0.126 AC XY: 9362 AN XY: 74364

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.0813

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0309

Gnomad4 NFE AF: 0.0631

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0555 Hom.: 100

Bravo AF: 0.137

Asia WGS AF: 0.190 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12218361; hg19: chr10-126070149;