rs722183

Variant names:

• chr11-7754315-C-T
• rs722183
• ENST00000527565.1:n.543-49641G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000527565.1(ENSG00000271758):​n.543-49641G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,112 control chromosomes in the GnomAD database, including 4,025 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 (4025 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000271758 ENST00000527565.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275

Genes affected

ENSG00000271758 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000271758	ENST00000527565.1	n.543-49641G>A		intron_variant	Intron 5 of 5	3
ENSG00000254951	ENST00000529488.5	n.*78G>A		downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27076 AN: 151994 Hom.: 3995 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.0697

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.0770

Gnomad OTH AF: 0.158

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 10 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.179 AC: 27155 AN: 152112 Hom.: 4025 Cov.: 32 AF XY: 0.177 AC XY: 13194 AN XY: 74364

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.0974

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.0697

Gnomad4 NFE AF: 0.0770

Gnomad4 OTH AF: 0.158

Alfa AF: 0.114 Hom.: 709

Bravo AF: 0.190

Asia WGS AF: 0.223 AC: 774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs722183; hg19: chr11-7775862;