4-76436339-C-A

Variant names:

• chr4-76436339-C-A
• rs554755626
• NM_020859.4:c.168+119C>A

Variant summary

Our verdict is Benign. The variant received -18 ACMG points: 0P and 18B. BP4_Moderate BP6_Very_Strong BA1

The NM_020859.4(SHROOM3):​c.168+119C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,116,882 control chromosomes in the GnomAD database, including 13,744 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.16 (1915 hom., cov: 32)
  • Exomes 𝑓: 0.15 (11829 hom.)
• Consequence: SHROOM3 NM_020859.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.328
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• neural tube defect

  Inheritance: AD Classification: STRONG Submitted by: G2P
• syndromic disease

  Inheritance: AR Classification: MODERATE Submitted by: PanelApp Australia

ACMG classification

Our verdict: Benign. The variant received -18 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BP6: Variant 4-76436339-C-A is Benign according to our data. Variant chr4-76436339-C-A is described in ClinVar as Benign. ClinVar VariationId is 1179242.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020859.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SHROOM3	NM_020859.4	MANE Select	c.168+119C>A		intron	N/A	NP_065910.3	Q8TF72-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SHROOM3	ENST00000296043.7	TSL:1 MANE Select	c.168+119C>A		intron	N/A	ENSP00000296043.6	Q8TF72-1
	SHROOM3	ENST00000912766.1		c.168+119C>A		intron	N/A	ENSP00000582825.1
	SHROOM3	ENST00000466541.1	TSL:3	n.75+119C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23956 AN: 151900 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: 0.197

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.171

GnomAD4 exome AF: 0.151 AC: 145521 AN: 964864 Hom.: 11829 AF XY: 0.154 AC XY: 76278 AN XY: 494954

African (AFR) AF: 0.152 AC: 3457 AN: 22758

American (AMR) AF: 0.0723 AC: 2513 AN: 34762

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 3619 AN: 20898

East Asian (EAS) AF: 0.162 AC: 5874 AN: 36178

South Asian (SAS) AF: 0.224 AC: 15011 AN: 67092

European-Finnish (FIN) AF: 0.183 AC: 8208 AN: 44876

Middle Eastern (MID) AF: 0.152 AC: 468 AN: 3078

European-Non Finnish (NFE) AF: 0.144 AC: 99554 AN: 691886

Other (OTH) AF: 0.157 AC: 6817 AN: 43336

GnomAD4 genome AF: 0.158 AC: 23963 AN: 152018 Hom.: 1915 Cov.: 32 AF XY: 0.158 AC XY: 11704 AN XY: 74300

African (AFR) AF: 0.152 AC: 6316 AN: 41458

American (AMR) AF: 0.105 AC: 1605 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 615 AN: 3470

East Asian (EAS) AF: 0.200 AC: 1038 AN: 5186

South Asian (SAS) AF: 0.234 AC: 1131 AN: 4824

European-Finnish (FIN) AF: 0.197 AC: 2069 AN: 10524

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10645 AN: 67964

Other (OTH) AF: 0.169 AC: 358 AN: 2114

Alfa AF: 0.0603 Hom.: 71

Asia WGS AF: 0.206 AC: 718 AN: 3476

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	8.6
DANN	Benign	0.63
PhyloP100		0.33
Mutation Taster		=98/2	polymorphism (auto)

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

Other links and lift over

dbSNP: rs554755626; hg19: chr4-77357492;