NM_020859.4:c.5349+1110C>T

Variant names:

• chr4-76760805-C-T
• rs17002201
• NM_020859.4:c.5349+1110C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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 = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHROOM3	NM_020859.4	c.5349+1110C>T		intron_variant	Intron 9 of 10	ENST00000296043.7	NP_065910.3
SHROOM3-AS1	NR_187404.1	n.408-2213G>A		intron_variant	Intron 1 of 3
SHROOM3-AS1	NR_187405.1	n.408-17905G>A		intron_variant	Intron 1 of 2
SHROOM3-AS1	NR_187406.1	n.97-2213G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SHROOM3	ENST00000296043.7	c.5349+1110C>T		intron_variant	Intron 9 of 10	1	NM_020859.4	ENSP00000296043.6

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

African (AFR) AF: 0.179 AC: 7419 AN: 41490

American (AMR) AF: 0.123 AC: 1887 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0744 AC: 258 AN: 3468

East Asian (EAS) AF: 0.217 AC: 1120 AN: 5158

South Asian (SAS) AF: 0.179 AC: 864 AN: 4826

European-Finnish (FIN) AF: 0.200 AC: 2113 AN: 10570

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

European-Non Finnish (NFE) AF: 0.112 AC: 7651 AN: 68014

Other (OTH) AF: 0.125 AC: 263 AN: 2112

Alfa AF: 0.123 Hom.: 366

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
PhyloP100		0.076
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: rs17002201; hg19: chr4-77681958;