chr1-96458541-C-T

Variant names:

• chr1-96458541-C-T
• rs11165643

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;