1-169504523-G-A

Variant names:

• chr1-169504523-G-A
• rs2420134

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 0.0568 in 152,198 control chromosomes in the GnomAD database, including 368 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 0.057 (368 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.097 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: 0.0568 AC: 8631 AN: 152080 Hom.: 367 Cov.: 32

Gnomad AFR AF: 0.0170

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0749

Gnomad EAS AF: 0.0296

Gnomad SAS AF: 0.0657

Gnomad FIN AF: 0.0862

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0673

Gnomad OTH AF: 0.0642

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

GnomAD4 genome AF: 0.0568 AC: 8640 AN: 152198 Hom.: 368 Cov.: 32 AF XY: 0.0590 AC XY: 4390 AN XY: 74418

African (AFR) AF: 0.0171 AC: 711 AN: 41550

American (AMR) AF: 0.101 AC: 1547 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0749 AC: 260 AN: 3470

East Asian (EAS) AF: 0.0297 AC: 154 AN: 5192

South Asian (SAS) AF: 0.0655 AC: 316 AN: 4824

European-Finnish (FIN) AF: 0.0862 AC: 911 AN: 10564

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0674 AC: 4582 AN: 68000

Other (OTH) AF: 0.0635 AC: 134 AN: 2110

Alfa AF: 0.0645 Hom.: 514

Bravo AF: 0.0529

Asia WGS AF: 0.0580 AC: 202 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.36
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2420134; hg19: chr1-169473761;