Variant chr4-76519114-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_020859.4(SHROOM3):c.169-36495T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 152,042 control chromosomes in the GnomAD database, including 30,429 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 0.62 ( 30429 hom., cov: 33)

Consequence

SHROOM3
NM_020859.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.38

Variant links:

Genes affected

SHROOM3 (HGNC:30422): (shroom family member 3) This gene encodes a PDZ-domain-containing protein that belongs to a family of Shroom-related proteins. This protein may be involved in regulating cell shape in certain tissues. A similar protein in mice is required for proper neurulation. [provided by RefSeq, Jan 2011]

SHROOM3 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 (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SHROOM3	NM_020859.4 link	c.169-36495T>C		intron_variant		ENST00000296043.7	NP_065910.3	Q8TF72-1B3KY47

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
SHROOM3	ENST00000296043.7 link	c.169-36495T>C	intron_variant	1	NM_020859.4	ENSP00000296043.6	Q8TF72-1
SHROOM3	ENST00000466541.1 link	n.76-36495T>C	intron_variant	3
SHROOM3	ENST00000497440.5 link	n.110-36495T>C	intron_variant	3

Frequencies

GnomAD3 genomes

AF:

0.618

AC:

93870

AN:

151924

Hom.:

30408

Cov.:

show subpopulations

Gnomad AFR

AF:

0.821

Gnomad AMI

AF:

0.706

Gnomad AMR

AF:

0.582

Gnomad ASJ

AF:

0.694

Gnomad EAS

AF:

0.575

Gnomad SAS

AF:

0.640

Gnomad FIN

AF:

0.501

Gnomad MID

AF:

0.775

Gnomad NFE

AF:

0.515

Gnomad OTH

AF:

0.644

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

GnomAD4 genome

AF:

0.618

AC:

93935

AN:

152042

Hom.:

30429

Cov.:

AF XY:

0.620

AC XY:

46073

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.820

Gnomad4 AMR

AF:

0.582

Gnomad4 ASJ

AF:

0.694

Gnomad4 EAS

AF:

0.575

Gnomad4 SAS

AF:

0.640

Gnomad4 FIN

AF:

0.501

Gnomad4 NFE

AF:

0.515

Gnomad4 OTH

AF:

0.645

Alfa

AF:

0.543

Hom.:

28519

Bravo

AF:

0.631

Asia WGS

AF:

0.638

AC:

2217

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

0.58

DANN

Benign

0.78

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