rs1150780

Variant names:

• chr6-34247451-G-A
• rs1150780
• NM_001008703.4:c.137+16C>T

Variant summary

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

The NM_001008703.4(SMIM29):​c.137+16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 1,573,726 control chromosomes in the GnomAD database, including 46,268 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 0.18 (3186 hom., cov: 32)
  • Exomes 𝑓: 0.24 (43082 hom.)
• Consequence: SMIM29 NM_001008703.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 7 publications found

Genes affected

SMIM29 (HGNC:1340): (small integral membrane protein 29) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMIM29	NM_001008703.4	c.137+16C>T		intron_variant	Intron 3 of 4	ENST00000476320.6	NP_001008703.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMIM29	ENST00000476320.6	c.137+16C>T		intron_variant	Intron 3 of 4	2	NM_001008703.4	ENSP00000417604.2

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27514 AN: 151772 Hom.: 3184 Cov.: 32

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.155

GnomAD2 exomes AF: 0.214 AC: 40545 AN: 189788 AF XY: 0.218

Gnomad AFR exome AF: 0.0377

Gnomad AMR exome AF: 0.167

Gnomad ASJ exome AF: 0.130

Gnomad EAS exome AF: 0.254

Gnomad FIN exome AF: 0.298

Gnomad NFE exome AF: 0.236

Gnomad OTH exome AF: 0.199

GnomAD4 exome AF: 0.241 AC: 342752 AN: 1421834 Hom.: 43082 Cov.: 34 AF XY: 0.240 AC XY: 169085 AN XY: 703070

African (AFR) AF: 0.0358 AC: 1188 AN: 33144

American (AMR) AF: 0.170 AC: 6600 AN: 38918

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 3279 AN: 25276

East Asian (EAS) AF: 0.229 AC: 8792 AN: 38366

South Asian (SAS) AF: 0.231 AC: 18655 AN: 80722

European-Finnish (FIN) AF: 0.295 AC: 14873 AN: 50456

Middle Eastern (MID) AF: 0.151 AC: 861 AN: 5710

European-Non Finnish (NFE) AF: 0.253 AC: 275327 AN: 1090366

Other (OTH) AF: 0.224 AC: 13177 AN: 58876

GnomAD4 genome AF: 0.181 AC: 27517 AN: 151892 Hom.: 3186 Cov.: 32 AF XY: 0.183 AC XY: 13597 AN XY: 74196

African (AFR) AF: 0.0473 AC: 1962 AN: 41486

American (AMR) AF: 0.167 AC: 2551 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1281 AN: 5134

South Asian (SAS) AF: 0.222 AC: 1068 AN: 4818

European-Finnish (FIN) AF: 0.311 AC: 3255 AN: 10472

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.243 AC: 16489 AN: 67934

Other (OTH) AF: 0.162 AC: 342 AN: 2110

Alfa AF: 0.210 Hom.: 2458

Bravo AF: 0.164

Asia WGS AF: 0.253 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.73
PhyloP100		0.10
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: rs1150780; hg19: chr6-34215228; COSMIC: COSV58988294; COSMIC: COSV58988294;