rs3217060

Positions:

• chr11-64304830-CGTGACCTTCATTCGGTCACCGCA-C
• chr11-64304830-CGTGACCTTCATTCGGTCACCGCA-CGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA
• chr11-64304830-CGTGACCTTCATTCGGTCACCGCA-CGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA
• chr11-64304830-CGTGACCTTCATTCGGTCACCGCA-CGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The variant allele was found at a frequency of 0.00103 in 544,824 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0010 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0010 (1 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.922

Genes affected

(HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.64304831_64304853delGTGACCTTCATTCGGTCACCGCA		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00103 AC: 155 AN: 150064 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00146

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000924

Gnomad ASJ AF: 0.00262

Gnomad EAS AF: 0.000789

Gnomad SAS AF: 0.00276

Gnomad FIN AF: 0.0000958

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000791

Gnomad OTH AF: 0.000484

GnomAD4 exome AF: 0.00103 AC: 407 AN: 394644 Hom.: 1 AF XY: 0.00128 AC XY: 265 AN XY: 207798

Gnomad4 AFR exome AF: 0.000791

Gnomad4 AMR exome AF: 0.000320

Gnomad4 ASJ exome AF: 0.00279

Gnomad4 EAS exome AF: 0.0000371

Gnomad4 SAS exome AF: 0.00451

Gnomad4 FIN exome AF: 0.0000771

Gnomad4 NFE exome AF: 0.000710

Gnomad4 OTH exome AF: 0.000565

GnomAD4 genome AF: 0.00103 AC: 155 AN: 150180 Hom.: 0 Cov.: 32 AF XY: 0.00109 AC XY: 80 AN XY: 73364

Gnomad4 AFR AF: 0.00146

Gnomad4 AMR AF: 0.000923

Gnomad4 ASJ AF: 0.00262

Gnomad4 EAS AF: 0.000791

Gnomad4 SAS AF: 0.00276

Gnomad4 FIN AF: 0.0000958

Gnomad4 NFE AF: 0.000791

Gnomad4 OTH AF: 0.000478

Alfa AF: 0.000125 Hom.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3217060; hg19: chr11-64072302;