chr1-155107614-A-G

Variant names:

• chr1-155107614-A-G
• rs7368345

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 0.595 in 152,100 control chromosomes in the GnomAD database, including 27,896 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 0.59 (27896 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90426 AN: 151982 Hom.: 27881 Cov.: 33

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.595 AC: 90479 AN: 152100 Hom.: 27896 Cov.: 33 AF XY: 0.595 AC XY: 44211 AN XY: 74352

African (AFR) AF: 0.730 AC: 30290 AN: 41500

American (AMR) AF: 0.624 AC: 9531 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1455 AN: 3472

East Asian (EAS) AF: 0.899 AC: 4660 AN: 5184

South Asian (SAS) AF: 0.548 AC: 2644 AN: 4828

European-Finnish (FIN) AF: 0.549 AC: 5798 AN: 10568

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34282 AN: 67954

Other (OTH) AF: 0.566 AC: 1194 AN: 2110

Alfa AF: 0.575 Hom.: 5027

Bravo AF: 0.610

Asia WGS AF: 0.706 AC: 2454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.5
DANN	Benign	0.65
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs7368345; hg19: chr1-155080090;