rs1198823

Variant names:

• chr2-237851475-A-G
• rs1198823

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 0.362 in 152,116 control chromosomes in the GnomAD database, including 10,146 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 0.36 (10146 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.417 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: 0.362 AC: 55000 AN: 151998 Hom.: 10141 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.362 AC: 55016 AN: 152116 Hom.: 10146 Cov.: 33 AF XY: 0.364 AC XY: 27071 AN XY: 74368

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.368

Alfa AF: 0.351 Hom.: 12790

Bravo AF: 0.361

Asia WGS AF: 0.276 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1198823; hg19: chr2-238760118;