1-96458541-C-T

Position:

• chr1-96458541-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 0.487 in 151,750 control chromosomes in the GnomAD database, including 20,489 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 0.49 (20489 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 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: 0.487 AC: 73876 AN: 151632 Hom.: 20480 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.487 AC: 73889 AN: 151750 Hom.: 20489 Cov.: 32 AF XY: 0.490 AC XY: 36304 AN XY: 74164

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.493

Alfa AF: 0.558 Hom.: 12830

Bravo AF: 0.478

Asia WGS AF: 0.663 AC: 2296 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11165643; hg19: chr1-96924097;