1-36639676-T-C

Position:

• chr1-36639676-T-C

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 0.574 in 152,198 control chromosomes in the GnomAD database, including 29,118 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 0.57 (29118 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.893 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: 0.574 AC: 87310 AN: 152080 Hom.: 29054 Cov.: 33

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.574 AC: 87430 AN: 152198 Hom.: 29118 Cov.: 33 AF XY: 0.579 AC XY: 43077 AN XY: 74410

Gnomad4 AFR AF: 0.885

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.915

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.584

Alfa AF: 0.316 Hom.: 1065

Bravo AF: 0.608

Asia WGS AF: 0.800 AC: 2780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10908312; hg19: chr1-37105277;