rs11889338

Variant names:

• chr2-17246318-G-A
• rs11889338

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 0.102 in 152,184 control chromosomes in the GnomAD database, including 1,841 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 0.10 (1841 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 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: 0.102 AC: 15482 AN: 152066 Hom.: 1840 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0988

Gnomad ASJ AF: 0.0381

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.0326

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0157

Gnomad OTH AF: 0.0804

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

GnomAD4 genome AF: 0.102 AC: 15509 AN: 152184 Hom.: 1841 Cov.: 33 AF XY: 0.100 AC XY: 7457 AN XY: 74416

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.0987

Gnomad4 ASJ AF: 0.0381

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.0328

Gnomad4 FIN AF: 0.0179

Gnomad4 NFE AF: 0.0157

Gnomad4 OTH AF: 0.0786

Alfa AF: 0.0280 Hom.: 263

Bravo AF: 0.118

Asia WGS AF: 0.0920 AC: 320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.61
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11889338; hg19: chr2-17427585;