rs1898705

Positions:

• chr2-118908386-G-A

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 0.0926 in 152,168 control chromosomes in the GnomAD database, including 725 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 0.093 (725 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.109 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: 0.0926 AC: 14083 AN: 152050 Hom.: 726 Cov.: 32

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0709

Gnomad FIN AF: 0.0896

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0949

Gnomad OTH AF: 0.0927

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

GnomAD4 genome AF: 0.0926 AC: 14096 AN: 152168 Hom.: 725 Cov.: 32 AF XY: 0.0920 AC XY: 6844 AN XY: 74386

Gnomad4 AFR AF: 0.0948

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0705

Gnomad4 FIN AF: 0.0896

Gnomad4 NFE AF: 0.0949

Gnomad4 OTH AF: 0.0913

Alfa AF: 0.0985 Hom.: 384

Bravo AF: 0.0960

Asia WGS AF: 0.0360 AC: 124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.012
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1898705; hg19: chr2-119665962;