1-197068537-A-G

Variant names:

• chr1-197068537-A-G
• rs1115247

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 0.777 in 151,970 control chromosomes in the GnomAD database, including 49,482 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 0.78 (49482 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.54
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118065 AN: 151852 Hom.: 49461 Cov.: 30

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.910

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.777 AC: 118136 AN: 151970 Hom.: 49482 Cov.: 30 AF XY: 0.783 AC XY: 58140 AN XY: 74282

African (AFR) AF: 0.428 AC: 17738 AN: 41400

American (AMR) AF: 0.870 AC: 13287 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.903 AC: 3132 AN: 3470

East Asian (EAS) AF: 0.996 AC: 5132 AN: 5152

South Asian (SAS) AF: 0.898 AC: 4301 AN: 4790

European-Finnish (FIN) AF: 0.929 AC: 9849 AN: 10606

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.910 AC: 61859 AN: 67974

Other (OTH) AF: 0.809 AC: 1702 AN: 2104

Alfa AF: 0.794 Hom.: 6821

Bravo AF: 0.757

Asia WGS AF: 0.918 AC: 3192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.24
DANN	Benign	0.12
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs1115247; hg19: chr1-197037667;