chr1-96034274-T-A

Variant names:

• chr1-96034274-T-A
• rs161115

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;