1-118660677-C-T

Position:

• chr1-118660677-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0991 in 152,086 control chromosomes in the GnomAD database, including 941 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 0.099 (941 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.38

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 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: 0.0991 AC: 15060 AN: 151968 Hom.: 941 Cov.: 32

Gnomad AFR AF: 0.0449

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0964

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0771

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0710

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.0991 AC: 15067 AN: 152086 Hom.: 941 Cov.: 32 AF XY: 0.0981 AC XY: 7292 AN XY: 74338

Gnomad4 AFR AF: 0.0448

Gnomad4 AMR AF: 0.0962

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.0769

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.0710

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.131

Alfa AF: 0.0635 Hom.: 84

Bravo AF: 0.0979

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	20
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12143914; hg19: chr1-119203300;