rs78540526

Positions:

• chr11-69516650-C-T

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 0.0523 in 152,252 control chromosomes in the GnomAD database, including 304 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 0.052 (304 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0922 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: 0.0523 AC: 7953 AN: 152134 Hom.: 306 Cov.: 33

Gnomad AFR AF: 0.0122

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0399

Gnomad ASJ AF: 0.0456

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.0995

Gnomad FIN AF: 0.0831

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0759

Gnomad OTH AF: 0.0460

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

GnomAD4 genome AF: 0.0523 AC: 7957 AN: 152252 Hom.: 304 Cov.: 33 AF XY: 0.0536 AC XY: 3987 AN XY: 74442

Gnomad4 AFR AF: 0.0121

Gnomad4 AMR AF: 0.0399

Gnomad4 ASJ AF: 0.0456

Gnomad4 EAS AF: 0.00290

Gnomad4 SAS AF: 0.0995

Gnomad4 FIN AF: 0.0831

Gnomad4 NFE AF: 0.0759

Gnomad4 OTH AF: 0.0484

Alfa AF: 0.0694 Hom.: 61

Bravo AF: 0.0438

Asia WGS AF: 0.0620 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.67
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs78540526; hg19: chr11-69331418;