rs1869410

Variant names:

• chr2-5117223-T-C
• rs1869410

Your query was ambiguous. Multiple possible variants found:

• chr2-5117223-T-C
• chr2-5117223-T-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 0.205 in 152,010 control chromosomes in the GnomAD database, including 3,998 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 0.20 (3998 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 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: 0.205 AC: 31173 AN: 151892 Hom.: 4004 Cov.: 32

Gnomad AFR AF: 0.0742

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.0130

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.205 AC: 31161 AN: 152010 Hom.: 3998 Cov.: 32 AF XY: 0.207 AC XY: 15393 AN XY: 74284

Gnomad4 AFR AF: 0.0741

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.0128

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.204

Alfa AF: 0.257 Hom.: 10980

Bravo AF: 0.184

Asia WGS AF: 0.133 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1869410; hg19: chr2-5257356;