Variant rs12404218 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The ENST00000669750.1(ENSG00000231424):n.533+77988A>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 0.103 in 152,248 control chromosomes in the GnomAD database, including 1,073 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.10 ( 1073 hom., cov: 32)

Consequence

ENST00000669750.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.243

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 1-171090116-T-A is Benign according to our data. Variant chr1-171090116-T-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Transcript	HGVSc	Effect
ENST00000669750.1 linkuse as main transcript	n.533+77988A>T	intron_variant, non_coding_transcript_variant
ENST00000653116.1 linkuse as main transcript	n.542+77988A>T	intron_variant, non_coding_transcript_variant
ENST00000664920.1 linkuse as main transcript	n.681+31634A>T	intron_variant, non_coding_transcript_variant
ENST00000670085.1 linkuse as main transcript	n.371+77988A>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15674

AN:

152130

Hom.:

1065

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.115

Gnomad AMR

AF:

0.202

Gnomad ASJ

AF:

0.0818

Gnomad EAS

AF:

0.215

Gnomad SAS

AF:

0.194

Gnomad FIN

AF:

0.0497

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.0622

Gnomad OTH

AF:

0.0989

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

GnomAD4 genome

AF:

0.103

AC:

15700

AN:

152248

Hom.:

1073

Cov.:

AF XY:

0.106

AC XY:

7888

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.124

Gnomad4 AMR

AF:

0.203

Gnomad4 ASJ

AF:

0.0818

Gnomad4 EAS

AF:

0.215

Gnomad4 SAS

AF:

0.194

Gnomad4 FIN

AF:

0.0497

Gnomad4 NFE

AF:

0.0622

Gnomad4 OTH

AF:

0.102

Alfa

AF:

0.0841

Hom.:

Bravo

AF:

0.114

Asia WGS

AF:

0.218

AC:

756

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.7

DANN

Benign

0.74

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