rs11889338

chr2-17246318-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 0.102 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;