11-85944062-A-C

Position:

• chr11-85944062-A-C

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 0.82 in 152,128 control chromosomes in the GnomAD database, including 51,283 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 0.82 (51283 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 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: 0.820 AC: 124583 AN: 152010 Hom.: 51242 Cov.: 32

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.820 AC: 124681 AN: 152128 Hom.: 51283 Cov.: 32 AF XY: 0.816 AC XY: 60693 AN XY: 74386

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.750

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.824

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.793

Alfa AF: 0.820 Hom.: 5974

Bravo AF: 0.818

Asia WGS AF: 0.709 AC: 2469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1237230; hg19: chr11-85655105;