rs1493360

Variant names:

• chr4-76704049-A-G
• rs1493360
• NM_020859.4:c.324-6107A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020859.4(SHROOM3):​c.324-6107A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,240 control chromosomes in the GnomAD database, including 1,599 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 0.13 (1599 hom., cov: 33)
• Consequence: SHROOM3 NM_020859.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 2 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-AS1 (HGNC:41265): (SHROOM3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHROOM3	NM_020859.4	c.324-6107A>G		intron_variant	Intron 2 of 10	ENST00000296043.7	NP_065910.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SHROOM3	ENST00000296043.7	c.324-6107A>G		intron_variant	Intron 2 of 10	1	NM_020859.4	ENSP00000296043.6

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19960 AN: 152122 Hom.: 1597 Cov.: 33

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0886

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.131 AC: 19988 AN: 152240 Hom.: 1599 Cov.: 33 AF XY: 0.132 AC XY: 9847 AN XY: 74442

African (AFR) AF: 0.202 AC: 8389 AN: 41526

American (AMR) AF: 0.119 AC: 1824 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3468

East Asian (EAS) AF: 0.207 AC: 1074 AN: 5176

South Asian (SAS) AF: 0.140 AC: 676 AN: 4824

European-Finnish (FIN) AF: 0.130 AC: 1380 AN: 10610

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0887 AC: 6032 AN: 68018

Other (OTH) AF: 0.106 AC: 225 AN: 2114

Alfa AF: 0.114 Hom.: 604

Bravo AF: 0.134

Asia WGS AF: 0.184 AC: 640 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	0.41
DANN	Benign	0.57
PhyloP100		-2.2
Mutation Taster		=100/0	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: rs1493360; hg19: chr4-77625202;