rs2290419

Positions:

• chr11-69152181-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_104161.1(LOC338694):​n.476-4441T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0483 in 151,768 control chromosomes in the GnomAD database, including 258 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 0.048 (258 hom., cov: 31)
• Consequence: LOC338694 NR_104161.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.739

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC338694	NR_104161.1	n.476-4441T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000562772.1	n.478-4441T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0484 AC: 7334 AN: 151650 Hom.: 258 Cov.: 31

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.0549

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0807

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0209

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0580

Gnomad OTH AF: 0.0671

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

GnomAD4 genome AF: 0.0483 AC: 7329 AN: 151768 Hom.: 258 Cov.: 31 AF XY: 0.0487 AC XY: 3604 AN XY: 74078

Gnomad4 AFR AF: 0.0137

Gnomad4 AMR AF: 0.0548

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.0799

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0209

Gnomad4 NFE AF: 0.0580

Gnomad4 OTH AF: 0.0659

Alfa AF: 0.0573 Hom.: 69

Bravo AF: 0.0473

Asia WGS AF: 0.101 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.4
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2290419; hg19: chr11-68919649;