rs4859682

Positions:

• chr4-76489165-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020859.4(SHROOM3):​c.168+52945C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,102 control chromosomes in the GnomAD database, including 9,664 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 0.33 (9664 hom., cov: 32)
• Consequence: SHROOM3 NM_020859.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SHROOM3	NM_020859.4	c.168+52945C>A		intron_variant		ENST00000296043.7	NP_065910.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SHROOM3	ENST00000296043.7	c.168+52945C>A		intron_variant		1	NM_020859.4	ENSP00000296043	P1
SHROOM3	ENST00000466541.1	n.75+52945C>A		intron_variant, non_coding_transcript_variant		3
SHROOM3	ENST00000497440.5	n.109+52945C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49725 AN: 151984 Hom.: 9660 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.327 AC: 49736 AN: 152102 Hom.: 9664 Cov.: 32 AF XY: 0.323 AC XY: 23984 AN XY: 74360

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.328

Alfa AF: 0.418 Hom.: 28413

Bravo AF: 0.317

Asia WGS AF: 0.181 AC: 631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.38
DANN	Benign	0.61

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

Other links and lift over

dbSNP: rs4859682; hg19: chr4-77410318;