Variant rs1551687 details in Genebe, Genetics Data Aggregator

Variant summary

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

The variant allele was found at a frequency of 0.423 in 151,520 control chromosomes in the GnomAD database, including 13,698 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 0.42 ( 13698 hom., cov: 33)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.07

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=-0.74).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
	use as main transcript	n.46223285A>C	intergenic_region
AHCYP1	use as main transcript	n.46223285A>C	intragenic_variant
ANTXRLP1	NR_103827.1 linkuse as main transcript	n.484-3579T>G	intron_variant
ANTXRLP1	NR_103828.1 linkuse as main transcript	n.304-3579T>G	intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.423

AC:

64002

AN:

151400

Hom.:

13671

Cov.:

show subpopulations

Gnomad AFR

AF:

0.527

Gnomad AMI

AF:

0.365

Gnomad AMR

AF:

0.491

Gnomad ASJ

AF:

0.443

Gnomad EAS

AF:

0.574

Gnomad SAS

AF:

0.290

Gnomad FIN

AF:

0.389

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.348

Gnomad OTH

AF:

0.418

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

GnomAD4 genome

AF:

0.423

AC:

64080

AN:

151520

Hom.:

13698

Cov.:

AF XY:

0.425

AC XY:

31472

AN XY:

74080

show subpopulations

Gnomad4 AFR

AF:

0.528

Gnomad4 AMR

AF:

0.491

Gnomad4 ASJ

AF:

0.443

Gnomad4 EAS

AF:

0.574

Gnomad4 SAS

AF:

0.289

Gnomad4 FIN

AF:

0.389

Gnomad4 NFE

AF:

0.348

Gnomad4 OTH

AF:

0.421

Alfa

AF:

0.386

Hom.:

1400

Bravo

AF:

0.441

Asia WGS

AF:

0.470

AC:

1634

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

2.3

DANN

Benign

0.35

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