1-160722754-T-G

Variant names:

• chr1-160722754-T-G
• rs570901

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 0.671 in 152,090 control chromosomes in the GnomAD database, including 34,432 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 0.67 (34432 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.754 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: 0.671 AC: 102020 AN: 151972 Hom.: 34401 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.671 AC: 102108 AN: 152090 Hom.: 34432 Cov.: 32 AF XY: 0.673 AC XY: 50060 AN XY: 74332

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.773

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.673

Alfa AF: 0.646 Hom.: 28697

Bravo AF: 0.679

Asia WGS AF: 0.767 AC: 2670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.78
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs570901; hg19: chr1-160692544;