chr1-162068986-G-A

Position:

• chr1-162068986-G-A

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 0.32 in 151,990 control chromosomes in the GnomAD database, including 8,235 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 0.32 (8235 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.609 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: 0.320 AC: 48622 AN: 151872 Hom.: 8233 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.320 AC: 48645 AN: 151990 Hom.: 8235 Cov.: 32 AF XY: 0.328 AC XY: 24346 AN XY: 74276

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.321

Alfa AF: 0.314 Hom.: 4199

Bravo AF: 0.308

Asia WGS AF: 0.574 AC: 1994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12090585; hg19: chr1-162038776;