dbSNP rs9387478: ENSG00000282218:c.547+101837G>T (chr6-117465017-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000467125.1(ENSG00000282218):c.547+101837G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 152,044 control chromosomes in the GnomAD database, including 29,122 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 0.60 ( 29122 hom., cov: 32)

Consequence

ENSG00000282218
ENST00000467125.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.406

Variant links:

Genes affected

ENSG00000282218 (HGNC:):

ENSG00000282218 links:

DCBLD1 (HGNC:21479): (discoidin, CUB and LCCL domain containing 1) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

DCBLD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
ENSG00000282218	ENST00000467125.1 link	c.547+101837G>T	intron_variant	Intron 4 of 6	2	ENSP00000487717.1	A0A0J9YVX5
DCBLD1	ENST00000525483.5 link	n.81+11120C>A	intron_variant	Intron 1 of 3	4
DCBLD1	ENST00000528138.5 link	n.191+852C>A	intron_variant	Intron 2 of 4	4
DCBLD1	ENST00000533950.1 link	n.64+11120C>A	intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.596

AC:

90595

AN:

151926

Hom.:

29075

Cov.:

show subpopulations

Gnomad AFR

AF:

0.853

Gnomad AMI

AF:

0.584

Gnomad AMR

AF:

0.451

Gnomad ASJ

AF:

0.435

Gnomad EAS

AF:

0.495

Gnomad SAS

AF:

0.686

Gnomad FIN

AF:

0.586

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.486

Gnomad OTH

AF:

0.554

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

GnomAD4 genome

AF:

0.597

AC:

90707

AN:

152044

Hom.:

29122

Cov.:

AF XY:

0.599

AC XY:

44513

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.853

Gnomad4 AMR

AF:

0.452

Gnomad4 ASJ

AF:

0.435

Gnomad4 EAS

AF:

0.495

Gnomad4 SAS

AF:

0.685

Gnomad4 FIN

AF:

0.586

Gnomad4 NFE

AF:

0.486

Gnomad4 OTH

AF:

0.553

Alfa

AF:

0.494

Hom.:

10011

Bravo

AF:

0.592

Asia WGS

AF:

0.604

AC:

2101

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.59

DANN

Benign

0.55

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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