chr11-69166429-T-C

Variant names:

• chr11-69166429-T-C
• rs1011176
• ENST00000562772.1:n.477+1900A>G

Variant summary

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

The ENST00000562772.1(ENSG00000261070):​n.477+1900A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,144 control chromosomes in the GnomAD database, including 14,121 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 0.42 (14121 hom., cov: 34)
• Consequence: ENSG00000261070 ENST00000562772.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 8 publications found

Genes affected

ENSG00000261070 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562772.1. 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
	LOC338694	NR_104161.1		n.475+1900A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261070	ENST00000562772.1	TSL:1	n.477+1900A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64182 AN: 152026 Hom.: 14108 Cov.: 34

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.424

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.422 AC: 64228 AN: 152144 Hom.: 14121 Cov.: 34 AF XY: 0.421 AC XY: 31334 AN XY: 74402

African (AFR) AF: 0.496 AC: 20608 AN: 41534

American (AMR) AF: 0.328 AC: 5011 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1806 AN: 3470

East Asian (EAS) AF: 0.427 AC: 2193 AN: 5138

South Asian (SAS) AF: 0.650 AC: 3134 AN: 4822

European-Finnish (FIN) AF: 0.308 AC: 3262 AN: 10602

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26876 AN: 67968

Other (OTH) AF: 0.424 AC: 896 AN: 2112

Alfa AF: 0.418 Hom.: 8188

Bravo AF: 0.420

Asia WGS AF: 0.487 AC: 1698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.78
DANN	Benign	0.36
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1011176; hg19: chr11-68933897;