2-197358397-T-C

Variant names:

• chr2-197358397-T-C
• rs787994

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 0.596 in 152,066 control chromosomes in the GnomAD database, including 27,798 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 0.60 (27798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.676 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: 0.596 AC: 90559 AN: 151948 Hom.: 27784 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.596 AC: 90605 AN: 152066 Hom.: 27798 Cov.: 32 AF XY: 0.596 AC XY: 44325 AN XY: 74312

African (AFR) AF: 0.457 AC: 18930 AN: 41446

American (AMR) AF: 0.599 AC: 9163 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2538 AN: 3472

East Asian (EAS) AF: 0.531 AC: 2743 AN: 5170

South Asian (SAS) AF: 0.696 AC: 3352 AN: 4818

European-Finnish (FIN) AF: 0.577 AC: 6098 AN: 10562

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45551 AN: 67992

Other (OTH) AF: 0.632 AC: 1337 AN: 2114

Alfa AF: 0.655 Hom.: 104165

Bravo AF: 0.585

Asia WGS AF: 0.605 AC: 2105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.9
DANN	Benign	0.69
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs787994; hg19: chr2-198223121;