chr11-5224277-G-A

Variant names:

• chr11-5224277-G-A
• rs10768682
• ENST00000408104.1:n.*171C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000408104.1(ENSG00000221031):​n.*171C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,046 control chromosomes in the GnomAD database, including 49,761 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 0.80 (49761 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000221031 ENST00000408104.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 4 publications found

Genes affected

ENSG00000221031 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000408104.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000221031	ENST00000408104.1	TSL:6	n.*171C>T		downstream_gene	N/A
	ENSG00000285498	ENST00000644706.1		n.*32C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122254 AN: 151928 Hom.: 49728 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.816

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.805 AC: 122340 AN: 152046 Hom.: 49761 Cov.: 32 AF XY: 0.796 AC XY: 59197 AN XY: 74332

African (AFR) AF: 0.855 AC: 35515 AN: 41518

American (AMR) AF: 0.720 AC: 11005 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2941 AN: 3466

East Asian (EAS) AF: 0.493 AC: 2540 AN: 5154

South Asian (SAS) AF: 0.619 AC: 2982 AN: 4816

European-Finnish (FIN) AF: 0.779 AC: 8179 AN: 10504

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56325 AN: 67994

Other (OTH) AF: 0.813 AC: 1716 AN: 2112

Alfa AF: 0.815 Hom.: 65017

Bravo AF: 0.809

Asia WGS AF: 0.565 AC: 1959 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.29
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs10768682; hg19: chr11-5245507;