5-171791134-G-T

Variant names:

• chr5-171791134-G-T
• rs7718767
• NM_001289970.2:c.*46G>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001289970.2(SMIM23):​c.*46G>T variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SMIM23 NM_001289970.2 splice_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

Genes affected

SMIM23 (HGNC:34440): (small integral membrane protein 23) Predicted to be located in plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMIM23	NM_001289970.2	c.*46G>T		splice_region_variant	Exon 4 of 4	ENST00000523047.4	NP_001276899.1
SMIM23	NM_001289970.2	c.*46G>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000523047.4	NP_001276899.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMIM23	ENST00000523047.4	c.*46G>T		splice_region_variant	Exon 4 of 4	2	NM_001289970.2	ENSP00000430818.4
SMIM23	ENST00000523047.4	c.*46G>T		3_prime_UTR_variant	Exon 4 of 4	2	NM_001289970.2	ENSP00000430818.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 26

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.2
DANN	Benign	0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7718767; hg19: chr5-171218138;