rs787994

Variant names:

• chr2-197358397-T-C
• rs787994

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 0.596 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.596 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

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.632

Alfa AF: 0.672 Hom.: 71547

Bravo AF: 0.585

Asia WGS AF: 0.605 AC: 2105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs787994; hg19: chr2-198223121;