rs11604821

Variant names:

• chr11-69537369-G-A
• rs11604821
• ENST00000807033.1:n.65+2878C>T

Variant summary

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

The ENST00000807033.1(ENSG00000304902):​n.65+2878C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,200 control chromosomes in the GnomAD database, including 21,342 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 (21342 hom., cov: 33)
• Consequence: ENSG00000304902 ENST00000807033.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 12 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.652 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+2878C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72234 AN: 152082 Hom.: 21346 Cov.: 33

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.475 AC: 72231 AN: 152200 Hom.: 21342 Cov.: 33 AF XY: 0.476 AC XY: 35450 AN XY: 74416

African (AFR) AF: 0.142 AC: 5914 AN: 41540

American (AMR) AF: 0.410 AC: 6266 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1793 AN: 3472

East Asian (EAS) AF: 0.241 AC: 1247 AN: 5180

South Asian (SAS) AF: 0.506 AC: 2439 AN: 4822

European-Finnish (FIN) AF: 0.766 AC: 8114 AN: 10590

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44679 AN: 67990

Other (OTH) AF: 0.467 AC: 987 AN: 2112

Alfa AF: 0.617 Hom.: 24709

Bravo AF: 0.432

Asia WGS AF: 0.375 AC: 1306 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	1.2
DANN	Benign	0.88
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs11604821; hg19: chr11-69352137;