1-197068537-A-G

Variant names:

• chr1-197068537-A-G
• rs1115247

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.777 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

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.870

Gnomad4 ASJ AF: 0.903

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.898

Gnomad4 FIN AF: 0.929

Gnomad4 NFE AF: 0.910

Gnomad4 OTH AF: 0.809

Alfa AF: 0.809 Hom.: 6743

Bravo AF: 0.757

Asia WGS AF: 0.918 AC: 3192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1115247; hg19: chr1-197037667;