chr11-65481674-A-G

Position:

• chr11-65481674-A-G

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 0.178 in 152,090 control chromosomes in the GnomAD database, including 2,566 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 0.18 (2566 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 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: 0.178 AC: 27069 AN: 151972 Hom.: 2560 Cov.: 31

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0839

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.178 AC: 27092 AN: 152090 Hom.: 2566 Cov.: 31 AF XY: 0.169 AC XY: 12600 AN XY: 74338

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0839

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.166

Alfa AF: 0.191 Hom.: 5273

Bravo AF: 0.187

Asia WGS AF: 0.120 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17146964; hg19: chr11-65249145;