1-160113222-C-T

Variant names:

• chr1-160113222-C-T
• rs4656879

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.802 in 152,092 control chromosomes in the GnomAD database, including 49,330 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 0.80 (49330 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 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: 0.802 AC: 121915 AN: 151974 Hom.: 49309 Cov.: 31

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.802 AC: 121984 AN: 152092 Hom.: 49330 Cov.: 31 AF XY: 0.803 AC XY: 59674 AN XY: 74358

African (AFR) AF: 0.693 AC: 28740 AN: 41444

American (AMR) AF: 0.818 AC: 12499 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2811 AN: 3472

East Asian (EAS) AF: 0.944 AC: 4887 AN: 5176

South Asian (SAS) AF: 0.899 AC: 4333 AN: 4822

European-Finnish (FIN) AF: 0.809 AC: 8569 AN: 10586

Middle Eastern (MID) AF: 0.771 AC: 225 AN: 292

European-Non Finnish (NFE) AF: 0.844 AC: 57415 AN: 68002

Other (OTH) AF: 0.807 AC: 1705 AN: 2112

Alfa AF: 0.837 Hom.: 97970

Bravo AF: 0.801

Asia WGS AF: 0.885 AC: 3078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.19
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs4656879; hg19: chr1-160083012;