rs11674899

Variant names:

• chr2-71155365-G-A
• rs11674899

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 0.164 in 151,974 control chromosomes in the GnomAD database, including 2,209 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 0.16 (2209 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.877

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.229 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: 0.164 AC: 24917 AN: 151856 Hom.: 2206 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.164 AC: 24937 AN: 151974 Hom.: 2209 Cov.: 32 AF XY: 0.167 AC XY: 12381 AN XY: 74264

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.171

Alfa AF: 0.174 Hom.: 1784

Bravo AF: 0.166

Asia WGS AF: 0.0710 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11674899; hg19: chr2-71382495;