rs11571300

chr2-203882044-A-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 0.106 in 152,132 control chromosomes in the GnomAD database, including 1,093 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 0.11 (1093 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.137 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: 0.106 AC: 16185 AN: 152014 Hom.: 1089 Cov.: 32

Gnomad AFR AF: 0.0287

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.106 AC: 16189 AN: 152132 Hom.: 1093 Cov.: 32 AF XY: 0.106 AC XY: 7887 AN XY: 74352

Gnomad4 AFR AF: 0.0286

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.130

Alfa AF: 0.134 Hom.: 1287

Bravo AF: 0.104

Asia WGS AF: 0.139 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	1.5
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11571300; hg19: chr2-204746767;