rs10820943

Positions:

• chr9-92154196-C-T

Variant summary

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

The NR_027341.1(LINC00475):​n.312+1332C>T 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 0.175 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: LINC00475 NR_027341.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC00475	NR_027341.1	n.312+1332C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000415471.2	n.91+3159G>A		intron_variant, non_coding_transcript_variant
	ENST00000416438.6	n.312+1332C>T		intron_variant, non_coding_transcript_variant		2
	ENST00000434944.1	n.164+1332C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.151

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10820943; hg19: chr9-94916478;