chr2-197351547-A-G

Variant names:

• chr2-197351547-A-G
• rs787997

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 0.588 in 151,968 control chromosomes in the GnomAD database, including 27,078 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 (27078 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.66 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: 0.588 AC: 89270 AN: 151850 Hom.: 27066 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.588 AC: 89308 AN: 151968 Hom.: 27078 Cov.: 32 AF XY: 0.588 AC XY: 43664 AN XY: 74268

African (AFR) AF: 0.440 AC: 18255 AN: 41446

American (AMR) AF: 0.597 AC: 9120 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2535 AN: 3472

East Asian (EAS) AF: 0.528 AC: 2724 AN: 5156

South Asian (SAS) AF: 0.676 AC: 3255 AN: 4812

European-Finnish (FIN) AF: 0.568 AC: 5987 AN: 10548

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45229 AN: 67960

Other (OTH) AF: 0.624 AC: 1312 AN: 2104

Alfa AF: 0.643 Hom.: 19859

Bravo AF: 0.578

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.57
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs787997; hg19: chr2-198216271;