chr1-156305490-G-A

Variant names:

• chr1-156305490-G-A
• rs7522860

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 0.455 in 151,914 control chromosomes in the GnomAD database, including 16,548 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 0.46 (16548 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69135 AN: 151796 Hom.: 16530 Cov.: 31

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.455 AC: 69189 AN: 151914 Hom.: 16548 Cov.: 31 AF XY: 0.457 AC XY: 33880 AN XY: 74214

African (AFR) AF: 0.310 AC: 12834 AN: 41432

American (AMR) AF: 0.587 AC: 8941 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1965 AN: 3468

East Asian (EAS) AF: 0.463 AC: 2393 AN: 5170

South Asian (SAS) AF: 0.535 AC: 2577 AN: 4818

European-Finnish (FIN) AF: 0.398 AC: 4182 AN: 10508

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34644 AN: 67960

Other (OTH) AF: 0.487 AC: 1028 AN: 2112

Alfa AF: 0.497 Hom.: 54258

Bravo AF: 0.464

Asia WGS AF: 0.525 AC: 1825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.73
DANN	Benign	0.15
PhyloP100		-0.10

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7522860; hg19: chr1-156275281;