ENST00000415471.2:n.91+3159G>A

Variant names:

• chr9-92154196-C-T
• rs10820943
• ENST00000415471.2:n.91+3159G>A

Variant summary

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

The ENST00000415471.2(ENSG00000236717):​n.91+3159G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,278 control chromosomes in the GnomAD database, including 2,649 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 0.18 (2649 hom., cov: 33)
• Consequence: ENSG00000236717 ENST00000415471.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855
• Publications: 2 publications found

Genes affected

ENSG00000236717 (HGNC:):

LINC00475 (HGNC:23569): (long intergenic non-protein coding RNA 475)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00475	NR_027341.1	n.312+1332C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000236717	ENST00000415471.2	n.91+3159G>A		intron_variant	Intron 1 of 1	6
ENSG00000290644	ENST00000416438.6	n.312+1332C>T		intron_variant	Intron 2 of 3	2
ENSG00000290644	ENST00000434944.1	n.164+1332C>T		intron_variant	Intron 2 of 5	3

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26645 AN: 152160 Hom.: 2644 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.175 AC: 26681 AN: 152278 Hom.: 2649 Cov.: 33 AF XY: 0.175 AC XY: 13023 AN XY: 74468

African (AFR) AF: 0.275 AC: 11444 AN: 41542

American (AMR) AF: 0.177 AC: 2705 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 425 AN: 3470

East Asian (EAS) AF: 0.115 AC: 596 AN: 5184

South Asian (SAS) AF: 0.211 AC: 1018 AN: 4826

European-Finnish (FIN) AF: 0.132 AC: 1401 AN: 10618

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8682 AN: 68012

Other (OTH) AF: 0.151 AC: 320 AN: 2116

Alfa AF: 0.163 Hom.: 282

Bravo AF: 0.182

Asia WGS AF: 0.168 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.32
PhyloP100		-0.85
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10820943; hg19: chr9-94916478;