rs12037343

chr1-218758563-G-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 0.0641 in 152,238 control chromosomes in the GnomAD database, including 708 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 0.064 (708 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 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: 0.0642 AC: 9765 AN: 152120 Hom.: 709 Cov.: 33

Gnomad AFR AF: 0.0306

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0815

Gnomad ASJ AF: 0.0783

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0505

Gnomad OTH AF: 0.0941

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

GnomAD4 genome AF: 0.0641 AC: 9766 AN: 152238 Hom.: 708 Cov.: 33 AF XY: 0.0678 AC XY: 5048 AN XY: 74440

Gnomad4 AFR AF: 0.0306

Gnomad4 AMR AF: 0.0819

Gnomad4 ASJ AF: 0.0783

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0470

Gnomad4 NFE AF: 0.0505

Gnomad4 OTH AF: 0.0936

Alfa AF: 0.0575 Hom.: 58

Bravo AF: 0.0670

Asia WGS AF: 0.248 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	4.7
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12037343; hg19: chr1-218931905;