1-155122682-A-G

Variant names:

• chr1-155122682-A-G
• rs11264329

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 0.569 in 152,062 control chromosomes in the GnomAD database, including 26,081 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 0.57 (26081 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 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: 0.569 AC: 86422 AN: 151944 Hom.: 26066 Cov.: 31

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.569 AC: 86478 AN: 152062 Hom.: 26081 Cov.: 31 AF XY: 0.566 AC XY: 42088 AN XY: 74328

African (AFR) AF: 0.748 AC: 31044 AN: 41478

American (AMR) AF: 0.598 AC: 9142 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1370 AN: 3472

East Asian (EAS) AF: 0.897 AC: 4651 AN: 5184

South Asian (SAS) AF: 0.528 AC: 2547 AN: 4824

European-Finnish (FIN) AF: 0.446 AC: 4712 AN: 10560

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31386 AN: 67958

Other (OTH) AF: 0.525 AC: 1105 AN: 2104

Alfa AF: 0.484 Hom.: 35951

Bravo AF: 0.591

Asia WGS AF: 0.676 AC: 2352 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	3.6
DANN	Benign	0.43
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs11264329; hg19: chr1-155095158;