chr1-53164859-A-G

Variant names:

• chr1-53164859-A-G
• rs1288335

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 0.117 in 152,104 control chromosomes in the GnomAD database, including 1,129 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 0.12 (1129 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 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: 0.117 AC: 17712 AN: 151986 Hom.: 1119 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0859

Gnomad AMR AF: 0.0870

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0720

Gnomad SAS AF: 0.0860

Gnomad FIN AF: 0.0939

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.117 AC: 17752 AN: 152104 Hom.: 1129 Cov.: 32 AF XY: 0.114 AC XY: 8474 AN XY: 74374

African (AFR) AF: 0.160 AC: 6654 AN: 41462

American (AMR) AF: 0.0869 AC: 1328 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 528 AN: 3472

East Asian (EAS) AF: 0.0719 AC: 372 AN: 5172

South Asian (SAS) AF: 0.0865 AC: 417 AN: 4820

European-Finnish (FIN) AF: 0.0939 AC: 994 AN: 10588

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7100 AN: 67990

Other (OTH) AF: 0.115 AC: 243 AN: 2108

Alfa AF: 0.110 Hom.: 591

Bravo AF: 0.119

Asia WGS AF: 0.0630 AC: 218 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	8.0
DANN	Benign	0.85
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1288335; hg19: chr1-53630531;