1-168393090-G-C

Position:

• chr1-168393090-G-C

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 0.0792 in 152,250 control chromosomes in the GnomAD database, including 604 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 0.079 (604 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.113 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: 0.0793 AC: 12057 AN: 152132 Hom.: 602 Cov.: 32

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0682

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0345

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.0792 AC: 12060 AN: 152250 Hom.: 604 Cov.: 32 AF XY: 0.0808 AC XY: 6017 AN XY: 74422

Gnomad4 AFR AF: 0.0275

Gnomad4 AMR AF: 0.0681

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0347

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0885

Alfa AF: 0.0378 Hom.: 36

Bravo AF: 0.0684

Asia WGS AF: 0.0840 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.83
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16860501; hg19: chr1-168362328;