chr1-160466663-A-G

Position:

• chr1-160466663-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 0.736 in 151,694 control chromosomes in the GnomAD database, including 41,159 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 0.74 (41159 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.772 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: 0.736 AC: 111487 AN: 151576 Hom.: 41115 Cov.: 28

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.736 AC: 111582 AN: 151694 Hom.: 41159 Cov.: 28 AF XY: 0.736 AC XY: 54527 AN XY: 74094

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.793

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.760

Alfa AF: 0.729 Hom.: 4750

Bravo AF: 0.732

Asia WGS AF: 0.736 AC: 2561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1249564; hg19: chr1-160436453;