rs1887210

Variant names:

• chr9-110837834-C-G
• rs1887210

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 0.272 in 152,028 control chromosomes in the GnomAD database, including 5,823 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 0.27 (5823 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.650
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 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: 0.272 AC: 41282 AN: 151910 Hom.: 5812 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.272 AC: 41337 AN: 152028 Hom.: 5823 Cov.: 32 AF XY: 0.269 AC XY: 19955 AN XY: 74296

African (AFR) AF: 0.316 AC: 13082 AN: 41398

American (AMR) AF: 0.315 AC: 4820 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1150 AN: 3470

East Asian (EAS) AF: 0.278 AC: 1436 AN: 5172

South Asian (SAS) AF: 0.260 AC: 1253 AN: 4824

European-Finnish (FIN) AF: 0.198 AC: 2100 AN: 10582

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16623 AN: 67982

Other (OTH) AF: 0.291 AC: 613 AN: 2110

Alfa AF: 0.261 Hom.: 653

Bravo AF: 0.289

Asia WGS AF: 0.268 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.56
DANN	Benign	0.74
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs1887210; hg19: chr9-113600114;