rs1898705

Variant names:

• chr2-118908386-G-A
• rs1898705

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0948 AC: 3935 AN: 41516

American (AMR) AF: 0.113 AC: 1727 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 399 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5176

South Asian (SAS) AF: 0.0705 AC: 340 AN: 4820

European-Finnish (FIN) AF: 0.0896 AC: 949 AN: 10592

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0949 AC: 6450 AN: 67998

Other (OTH) AF: 0.0913 AC: 193 AN: 2114

Alfa AF: 0.0981 Hom.: 424

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
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1898705; hg19: chr2-119665962;