rs1198823

Positions:

• chr2-237851475-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;