11-69535077-C-T

Variant names:

• chr11-69535077-C-T
• rs11607932
• ENST00000807033.1:n.65+5170G>A

Variant summary

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

The ENST00000807033.1(ENSG00000304902):​n.65+5170G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,894 control chromosomes in the GnomAD database, including 21,271 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 0.47 (21271 hom., cov: 31)
• Consequence: ENSG00000304902 ENST00000807033.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.994
• Publications: 6 publications found

Genes affected

ENSG00000304902 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.653 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
ENSG00000304902	ENST00000807033.1	n.65+5170G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71878 AN: 151778 Hom.: 21277 Cov.: 31

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.473 AC: 71869 AN: 151894 Hom.: 21271 Cov.: 31 AF XY: 0.474 AC XY: 35175 AN XY: 74242

African (AFR) AF: 0.142 AC: 5873 AN: 41394

American (AMR) AF: 0.418 AC: 6382 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1854 AN: 3466

East Asian (EAS) AF: 0.169 AC: 870 AN: 5148

South Asian (SAS) AF: 0.516 AC: 2478 AN: 4806

European-Finnish (FIN) AF: 0.750 AC: 7915 AN: 10558

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.658 AC: 44713 AN: 67938

Other (OTH) AF: 0.471 AC: 993 AN: 2108

Alfa AF: 0.595 Hom.: 30923

Bravo AF: 0.432

Asia WGS AF: 0.355 AC: 1240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.052
DANN	Benign	0.30
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs11607932; hg19: chr11-69349845;