chr1-168532215-A-G

Position:

• chr1-168532215-A-G

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 0.58 in 152,142 control chromosomes in the GnomAD database, including 26,324 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 0.58 (26324 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 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: 0.580 AC: 88213 AN: 152024 Hom.: 26287 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.580 AC: 88306 AN: 152142 Hom.: 26324 Cov.: 32 AF XY: 0.592 AC XY: 44048 AN XY: 74384

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.603

Alfa AF: 0.513 Hom.: 26875

Bravo AF: 0.584

Asia WGS AF: 0.751 AC: 2613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10429892; hg19: chr1-168501453;