rs17002201

chr4-76760805-C-T

Variant summary

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

The NM_020859.4(SHROOM3):c.5349+1110C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,130 control chromosomes in the GnomAD database, including 1,713 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 0.14 (1713 hom., cov: 32)
• Consequence: SHROOM3 NM_020859.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

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]

(HGNC:):

SHROOM3-AS1 (HGNC:41265): (SHROOM3 antisense RNA 1)

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 (EAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SHROOM3	NM_020859.4	c.5349+1110C>T		intron_variant		ENST00000296043.7
SHROOM3-AS1	XR_938903.3	n.518-2213G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SHROOM3	ENST00000296043.7	c.5349+1110C>T		intron_variant		1	NM_020859.4	P1
	ENST00000449007.1	n.72-2213G>A		intron_variant, non_coding_transcript_variant		3
SHROOM3-AS1	ENST00000666924.1	n.356-17905G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21722 AN: 152012 Hom.: 1705 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0744

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.143 AC: 21771 AN: 152130 Hom.: 1713 Cov.: 32 AF XY: 0.147 AC XY: 10948 AN XY: 74366

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0744

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.125

Alfa AF: 0.122 Hom.: 353

Bravo AF: 0.139

Asia WGS AF: 0.189 AC: 657 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	3.5
Dann	Benign	0.43

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: rs17002201; hg19: chr4-77681958;