rs78540526

Variant names:

• chr11-69516650-C-T
• rs78540526

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 32 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0121 AC: 505 AN: 41564

American (AMR) AF: 0.0399 AC: 610 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0456 AC: 158 AN: 3466

East Asian (EAS) AF: 0.00290 AC: 15 AN: 5178

South Asian (SAS) AF: 0.0995 AC: 479 AN: 4812

European-Finnish (FIN) AF: 0.0831 AC: 882 AN: 10612

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0759 AC: 5161 AN: 68008

Other (OTH) AF: 0.0484 AC: 102 AN: 2108

Alfa AF: 0.0640 Hom.: 557

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs78540526; hg19: chr11-69331418;