chr1-96034274-T-A

Position:

• chr1-96034274-T-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.388 in 151,606 control chromosomes in the GnomAD database, including 11,811 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.39 (11811 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.47 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: 0.388 AC: 58852 AN: 151486 Hom.: 11801 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.388 AC: 58886 AN: 151606 Hom.: 11811 Cov.: 32 AF XY: 0.387 AC XY: 28645 AN XY: 74088

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.387

Alfa AF: 0.386 Hom.: 1459

Bravo AF: 0.393

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Uncertain	-0.080
CADD	Benign	19
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs161115; hg19: chr1-96499830;