chr5-171791134-G-A

Position:

• chr5-171791134-G-A

Variant summary

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

The NM_001289970.2(SMIM23):​c.*46G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 1,437,876 control chromosomes in the GnomAD database, including 118,920 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 0.36 (10328 hom., cov: 33)
  • Exomes 𝑓: 0.41 (108592 hom.)
• Consequence: SMIM23 NM_001289970.2 3_prime_UTR
• 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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMIM23	NM_001289970.2	c.*46G>A		3_prime_UTR_variant	4/4	ENST00000523047.4
SMIM23	XM_011534622.1	c.*46G>A		3_prime_UTR_variant	4/4
SMIM23	XM_011534623.2	c.*46G>A		3_prime_UTR_variant	4/4
SMIM23	XM_011534624.2	c.*46G>A		3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMIM23	ENST00000523047.4	c.*46G>A		3_prime_UTR_variant	4/4	2	NM_001289970.2	P1
SMIM23	ENST00000640082.1	n.788G>A		non_coding_transcript_exon_variant	4/4	5
SMIM23	ENST00000639838.1	c.*46G>A		3_prime_UTR_variant, NMD_transcript_variant	4/8	5

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54318 AN: 151968 Hom.: 10321 Cov.: 33

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.359

GnomAD4 exome AF: 0.406 AC: 522648 AN: 1285790 Hom.: 108592 Cov.: 26 AF XY: 0.402 AC XY: 251492 AN XY: 624846

Gnomad4 AFR exome AF: 0.221

Gnomad4 AMR exome AF: 0.338

Gnomad4 ASJ exome AF: 0.451

Gnomad4 EAS exome AF: 0.470

Gnomad4 SAS exome AF: 0.221

Gnomad4 FIN exome AF: 0.484

Gnomad4 NFE exome AF: 0.420

Gnomad4 OTH exome AF: 0.394

GnomAD4 genome AF: 0.357 AC: 54351 AN: 152086 Hom.: 10328 Cov.: 33 AF XY: 0.362 AC XY: 26906 AN XY: 74340

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.359

Alfa AF: 0.361 Hom.: 5103

Bravo AF: 0.349

Asia WGS AF: 0.346 AC: 1204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	3.1
DANN	Benign	0.91

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: rs7718767; hg19: chr5-171218138;