rs1863196

Positions:

• chr2-165701000-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 0.387 in 152,046 control chromosomes in the GnomAD database, including 12,717 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 0.39 (12717 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58847 AN: 151928 Hom.: 12710 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.387 AC: 58867 AN: 152046 Hom.: 12717 Cov.: 32 AF XY: 0.391 AC XY: 29028 AN XY: 74318

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.394

Alfa AF: 0.435 Hom.: 1925

Bravo AF: 0.363

Asia WGS AF: 0.322 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1863196; hg19: chr2-166557510;