1-40779682-C-T

Position:

• chr1-40779682-C-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 0.397 in 151,976 control chromosomes in the GnomAD database, including 12,086 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 0.40 (12086 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.514 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: 0.397 AC: 60220 AN: 151858 Hom.: 12074 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.397 AC: 60263 AN: 151976 Hom.: 12086 Cov.: 31 AF XY: 0.400 AC XY: 29690 AN XY: 74264

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.411

Alfa AF: 0.368 Hom.: 12601

Bravo AF: 0.398

Asia WGS AF: 0.516 AC: 1794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2769255; hg19: chr1-41245354;