chr11-86073937-A-C

Variant names:

• chr11-86073937-A-C
• rs638509

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 0.384 in 152,070 control chromosomes in the GnomAD database, including 11,449 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 0.38 (11449 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 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: 0.384 AC: 58420 AN: 151952 Hom.: 11444 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.384 AC: 58447 AN: 152070 Hom.: 11449 Cov.: 32 AF XY: 0.382 AC XY: 28410 AN XY: 74364

African (AFR) AF: 0.379 AC: 15701 AN: 41458

American (AMR) AF: 0.420 AC: 6423 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1195 AN: 3468

East Asian (EAS) AF: 0.485 AC: 2513 AN: 5182

South Asian (SAS) AF: 0.470 AC: 2266 AN: 4824

European-Finnish (FIN) AF: 0.270 AC: 2853 AN: 10578

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26229 AN: 67964

Other (OTH) AF: 0.367 AC: 774 AN: 2110

Alfa AF: 0.385 Hom.: 12785

Bravo AF: 0.392

Asia WGS AF: 0.446 AC: 1553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.39
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs638509; hg19: chr11-85784979;