11-64778919-C-T

Position:

• chr11-64778919-C-T

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 0.725 in 167,946 control chromosomes in the GnomAD database, including 48,517 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 0.71 (42967 hom., cov: 31)
  • Exomes 𝑓: 0.82 (5550 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.64778919C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SF1-DT	ENST00000594089.1	n.-35C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108588 AN: 151914 Hom.: 42968 Cov.: 31

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.750

GnomAD4 exome AF: 0.823 AC: 13095 AN: 15914 Hom.: 5550 Cov.: 0 AF XY: 0.827 AC XY: 6899 AN XY: 8346

Gnomad4 AFR exome AF: 0.317

Gnomad4 AMR exome AF: 0.610

Gnomad4 ASJ exome AF: 0.839

Gnomad4 EAS exome AF: 0.544

Gnomad4 SAS exome AF: 0.723

Gnomad4 FIN exome AF: 0.876

Gnomad4 NFE exome AF: 0.889

Gnomad4 OTH exome AF: 0.809

GnomAD4 genome AF: 0.714 AC: 108619 AN: 152032 Hom.: 42967 Cov.: 31 AF XY: 0.714 AC XY: 53053 AN XY: 74332

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.850

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.784

Gnomad4 FIN AF: 0.888

Gnomad4 NFE AF: 0.898

Gnomad4 OTH AF: 0.748

Alfa AF: 0.869 Hom.: 56831

Bravo AF: 0.684

Asia WGS AF: 0.686 AC: 2383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	2.9
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs606458; hg19: chr11-64546391;