chr1-58637536-C-G

Variant names:

• chr1-58637536-C-G
• rs12136988

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 0.217 in 152,042 control chromosomes in the GnomAD database, including 4,456 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 0.22 (4456 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 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: 0.218 AC: 33066 AN: 151924 Hom.: 4453 Cov.: 33

Gnomad AFR AF: 0.0550

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.217 AC: 33066 AN: 152042 Hom.: 4456 Cov.: 33 AF XY: 0.220 AC XY: 16330 AN XY: 74344

Gnomad4 AFR AF: 0.0548

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.250

Alfa AF: 0.242 Hom.: 623

Bravo AF: 0.213

Asia WGS AF: 0.257 AC: 894 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	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12136988; hg19: chr1-59103208;