rs12410279

Positions:

• chr1-220678178-A-G
• chr1-220678178-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 0.129 in 151,940 control chromosomes in the GnomAD database, including 1,863 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 (1863 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19583 AN: 151822 Hom.: 1859 Cov.: 31

Gnomad AFR AF: 0.0321

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.129 AC: 19587 AN: 151940 Hom.: 1863 Cov.: 31 AF XY: 0.135 AC XY: 10016 AN XY: 74242

Gnomad4 AFR AF: 0.0320

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.135

Alfa AF: 0.143 Hom.: 2989

Bravo AF: 0.137

Asia WGS AF: 0.237 AC: 813 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
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: rs12410279; hg19: chr1-220851520;