chr12-11173205-G-A

Variant names:

• chr12-11173205-G-A
• rs2416549
• NM_001271592.2:c.*1642G>A

Variant summary

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

The NM_001271592.2(SMIM10L1):​c.*1642G>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 0.512 in 151,976 control chromosomes in the GnomAD database, including 22,158 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 0.51 (22158 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SMIM10L1 NM_001271592.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 8 publications found

Genes affected

SMIM10L1 (HGNC:49847): (small integral membrane protein 10 like 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMIM10L1	NM_001271592.2	c.*1642G>A		3_prime_UTR_variant	Exon 1 of 1	ENST00000622602.2	NP_001258521.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMIM10L1	ENST00000622602.2	c.*1642G>A		3_prime_UTR_variant	Exon 1 of 1	6	NM_001271592.2	ENSP00000488907.1

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77742 AN: 151858 Hom.: 22154 Cov.: 31

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.543

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.512 AC: 77755 AN: 151976 Hom.: 22158 Cov.: 31 AF XY: 0.519 AC XY: 38575 AN XY: 74286

African (AFR) AF: 0.240 AC: 9941 AN: 41450

American (AMR) AF: 0.596 AC: 9112 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2246 AN: 3466

East Asian (EAS) AF: 0.743 AC: 3841 AN: 5172

South Asian (SAS) AF: 0.648 AC: 3119 AN: 4814

European-Finnish (FIN) AF: 0.668 AC: 7052 AN: 10562

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40469 AN: 67918

Other (OTH) AF: 0.546 AC: 1153 AN: 2112

Alfa AF: 0.566 Hom.: 10561

Bravo AF: 0.496

Asia WGS AF: 0.651 AC: 2259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.69
PhyloP100		0.091

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: rs2416549; hg19: chr12-11325804;