rs11823971

Positions:

• chr11-72677517-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 0.12 in 152,168 control chromosomes in the GnomAD database, including 1,240 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 0.12 (1240 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.503

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18315 AN: 152050 Hom.: 1238 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0711

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0865

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.120 AC: 18334 AN: 152168 Hom.: 1240 Cov.: 32 AF XY: 0.123 AC XY: 9139 AN XY: 74390

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.0711

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.0865

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0966 Hom.: 413

Bravo AF: 0.123

Asia WGS AF: 0.130 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.3
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11823971; hg19: chr11-72388561;