rs17121510

Variant names:

• chr11-118005440-A-G
• rs17121510
• NM_001394165.1:c.*970T>C

Variant summary

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

The NM_001394165.1(SMIM35):​c.*970T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,180 control chromosomes in the GnomAD database, including 1,929 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 0.15 (1927 hom., cov: 32)
  • Exomes 𝑓: 0.13 (2 hom.)
• Consequence: SMIM35 NM_001394165.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677
• Publications: 13 publications found

Genes affected

SMIM35 (HGNC:44179): (small integral membrane protein 35) 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=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394165.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMIM35	NM_001394165.1	MANE Select	c.*970T>C		3_prime_UTR	Exon 5 of 5	NP_001381094.1	A0A1B0GVV1
	SMIM35	NM_001394164.1		c.*970T>C		3_prime_UTR	Exon 6 of 6	NP_001381093.1
	SMIM35	NM_001394166.1		c.*970T>C		3_prime_UTR	Exon 4 of 4	NP_001381095.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMIM35	ENST00000689828.1	MANE Select	c.*970T>C		3_prime_UTR	Exon 5 of 5	ENSP00000509259.1	A0A1B0GVV1
	SMIM35	ENST00000636151.1	TSL:5	c.*1014T>C		3_prime_UTR	Exon 7 of 7	ENSP00000490666.1	A0A1B0GVV1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22110 AN: 151970 Hom.: 1925 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0436

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.149

GnomAD4 exome AF: 0.130 AC: 12 AN: 92 Hom.: 2 Cov.: 0 AF XY: 0.153 AC XY: 11 AN XY: 72

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.500 AC: 2 AN: 4

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0946 AC: 7 AN: 74

Other (OTH) AF: 0.167 AC: 1 AN: 6

GnomAD4 genome AF: 0.146 AC: 22137 AN: 152088 Hom.: 1927 Cov.: 32 AF XY: 0.145 AC XY: 10802 AN XY: 74342

African (AFR) AF: 0.239 AC: 9894 AN: 41462

American (AMR) AF: 0.120 AC: 1834 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 381 AN: 3468

East Asian (EAS) AF: 0.0437 AC: 226 AN: 5168

South Asian (SAS) AF: 0.104 AC: 500 AN: 4822

European-Finnish (FIN) AF: 0.117 AC: 1233 AN: 10582

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7460 AN: 67982

Other (OTH) AF: 0.148 AC: 313 AN: 2110

Alfa AF: 0.120 Hom.: 4120

Bravo AF: 0.148

Asia WGS AF: 0.0840 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	4.8
DANN	Benign	0.88
PhyloP100		-0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17121510; hg19: chr11-117876155;