chr11-643683-T-C

Position:

• chr11-643683-T-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 0.509 in 152,106 control chromosomes in the GnomAD database, including 20,003 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 0.51 (20003 hom., cov: 34)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.643683T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77396 AN: 151988 Hom.: 19980 Cov.: 34

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.509 AC: 77469 AN: 152106 Hom.: 20003 Cov.: 34 AF XY: 0.512 AC XY: 38099 AN XY: 74366

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.509

Alfa AF: 0.501 Hom.: 3220

Bravo AF: 0.511

Asia WGS AF: 0.627 AC: 2181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.36
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4331145; hg19: chr11-643683;