11-69166429-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000261070 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC338694	NR_104161.1	n.475+1900A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261070	ENST00000562772.1	n.477+1900A>G		intron_variant	Intron 2 of 2	1

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

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.424

Alfa AF: 0.418 Hom.: 7241

Bravo AF: 0.420

Asia WGS AF: 0.487 AC: 1698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1011176; hg19: chr11-68933897;