rs1272496

Variant names:

• chr11-130504156-G-A
• rs1272496

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 0.208 in 152,092 control chromosomes in the GnomAD database, including 3,614 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 0.21 (3614 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 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: 0.208 AC: 31614 AN: 151974 Hom.: 3614 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.00867

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.208 AC: 31626 AN: 152092 Hom.: 3614 Cov.: 32 AF XY: 0.204 AC XY: 15166 AN XY: 74352

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.00869

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.240

Alfa AF: 0.223 Hom.: 494

Bravo AF: 0.209

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	11
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1272496; hg19: chr11-130374051;