rs4627080

Positions:

• chr11-9314802-T-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 0.128 in 205,604 control chromosomes in the GnomAD database, including 2,333 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 0.14 (2007 hom., cov: 35)
  • Exomes 𝑓: 0.099 (326 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 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: 0.139 AC: 21100 AN: 152146 Hom.: 2005 Cov.: 35

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.0849

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0757

Gnomad OTH AF: 0.139

GnomAD4 exome AF: 0.0990 AC: 5283 AN: 53340 Hom.: 326 Cov.: 0 AF XY: 0.102 AC XY: 2816 AN XY: 27492

Gnomad4 AFR exome AF: 0.247

Gnomad4 AMR exome AF: 0.161

Gnomad4 ASJ exome AF: 0.125

Gnomad4 EAS exome AF: 0.119

Gnomad4 SAS exome AF: 0.186

Gnomad4 FIN exome AF: 0.0748

Gnomad4 NFE exome AF: 0.0753

Gnomad4 OTH exome AF: 0.121

GnomAD4 genome AF: 0.139 AC: 21131 AN: 152264 Hom.: 2007 Cov.: 35 AF XY: 0.140 AC XY: 10391 AN XY: 74448

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.0849

Gnomad4 NFE AF: 0.0757

Gnomad4 OTH AF: 0.139

Alfa AF: 0.113 Hom.: 213

Bravo AF: 0.148

Asia WGS AF: 0.161 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	7.2
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4627080; hg19: chr11-9336349;