4-76436338-C-CT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_020859.4(SHROOM3):c.168+118_168+119insT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 1,127,024 control chromosomes in the GnomAD database, including 13,732 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.16 (1915 hom., cov: 32)
  • Exomes 𝑓: 0.15 (11817 hom.)
• Consequence: SHROOM3 NM_020859.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.328

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 -10 ACMG points.

• BP6: Variant 4-76436338-C-CT is Benign according to our data. Variant chr4-76436338-C-CT is described in ClinVar as [Benign]. Clinvar id is 1289955.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SHROOM3	NM_020859.4	c.168+118_168+119insT		intron_variant		ENST00000296043.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SHROOM3	ENST00000296043.7	c.168+118_168+119insT		intron_variant		1	NM_020859.4	P1
SHROOM3	ENST00000466541.1	n.75+118_75+119insT		intron_variant, non_coding_transcript_variant		3
SHROOM3	ENST00000497440.5	n.109+118_109+119insT		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23955 AN: 151908 Hom.: 1911 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.171

GnomAD4 exome AF: 0.149 AC: 145187 AN: 974998 Hom.: 11817 AF XY: 0.152 AC XY: 76155 AN XY: 500006

Gnomad4 AFR exome AF: 0.150

Gnomad4 AMR exome AF: 0.0715

Gnomad4 ASJ exome AF: 0.172

Gnomad4 EAS exome AF: 0.162

Gnomad4 SAS exome AF: 0.222

Gnomad4 FIN exome AF: 0.182

Gnomad4 NFE exome AF: 0.142

Gnomad4 OTH exome AF: 0.156

GnomAD4 genome AF: 0.158 AC: 23962 AN: 152026 Hom.: 1915 Cov.: 32 AF XY: 0.158 AC XY: 11702 AN XY: 74288

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.170

Alfa AF: 0.0480 Hom.: 71

Asia WGS AF: 0.206 AC: 718 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

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: rs200881265; hg19: chr4-77357491;