Variant rs9356970 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_110863.1(LOC101928663):n.513+2610C>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 0.286 in 152,202 control chromosomes in the GnomAD database, including 7,886 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 0.29 ( 7886 hom., cov: 33)

Consequence

LOC101928663
NR_110863.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.323

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928663	NR_110863.1 linkuse as main transcript	n.513+2610C>T		intron_variant, non_coding_transcript_variant
LOC101928663	NR_110862.1 linkuse as main transcript	n.514-2432C>T		intron_variant, non_coding_transcript_variant

Ensembl

Transcript	HGVSc	Effect	TSL
ENST00000413898.2 linkuse as main transcript	n.518-2432C>T	intron_variant, non_coding_transcript_variant	1
ENST00000643807.1 linkuse as main transcript	n.364+112208C>T	intron_variant, non_coding_transcript_variant
ENST00000643481.1 linkuse as main transcript	n.517-2432C>T	intron_variant, non_coding_transcript_variant
ENST00000643656.2 linkuse as main transcript	n.267-2432C>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.286

AC:

43473

AN:

152086

Hom.:

7882

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0717

Gnomad AMI

AF:

0.439

Gnomad AMR

AF:

0.331

Gnomad ASJ

AF:

0.320

Gnomad EAS

AF:

0.612

Gnomad SAS

AF:

0.461

Gnomad FIN

AF:

0.454

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.340

Gnomad OTH

AF:

0.262

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

GnomAD4 genome

AF:

0.286

AC:

43477

AN:

152202

Hom.:

7886

Cov.:

AF XY:

0.298

AC XY:

22158

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.0715

Gnomad4 AMR

AF:

0.332

Gnomad4 ASJ

AF:

0.320

Gnomad4 EAS

AF:

0.614

Gnomad4 SAS

AF:

0.460

Gnomad4 FIN

AF:

0.454

Gnomad4 NFE

AF:

0.340

Gnomad4 OTH

AF:

0.264

Alfa

AF:

0.308

Hom.:

7518

Bravo

AF:

0.262

Asia WGS

AF:

0.467

AC:

1622

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.3

DANN

Benign

0.75

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over