rs10450321

Variant names:

• chr10-37337931-T-C
• rs10450321
• ENST00000457388.1:n.517T>C

Variant summary

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

The ENST00000457388.1(TMEM161BP1):​n.517T>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0733 in 1,497,384 control chromosomes in the GnomAD database, including 4,448 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 0.089 (753 hom., cov: 32)
  • Exomes 𝑓: 0.071 (3695 hom.)
• Consequence: TMEM161BP1 ENST00000457388.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.55
• Publications: 1 publications found

Genes affected

TMEM161BP1 (HGNC:44973): (transmembrane protein 161B pseudogene 1)

ENSG00000290801 (HGNC:):

LINC00993 (HGNC:48948): (long intergenic non-protein coding RNA 993)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000457388.1. 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
	LINC00993	NR_104061.1		n.314-4395T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM161BP1	ENST00000457388.1	TSL:6	n.517T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000290801	ENST00000426471.6	TSL:2	n.315-4395T>C		intron	N/A
	ENSG00000290801	ENST00000435629.5	TSL:3	n.204-4395T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0887 AC: 13497 AN: 152096 Hom.: 727 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.0598

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.0987

Gnomad SAS AF: 0.0735

Gnomad FIN AF: 0.0457

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0689

Gnomad OTH AF: 0.0943

GnomAD4 exome AF: 0.0715 AC: 96153 AN: 1345170 Hom.: 3695 Cov.: 23 AF XY: 0.0708 AC XY: 47894 AN XY: 676158

African (AFR) AF: 0.150 AC: 4683 AN: 31206

American (AMR) AF: 0.0647 AC: 2877 AN: 44474

Ashkenazi Jewish (ASJ) AF: 0.0662 AC: 1683 AN: 25404

East Asian (EAS) AF: 0.0941 AC: 3685 AN: 39140

South Asian (SAS) AF: 0.0655 AC: 5484 AN: 83726

European-Finnish (FIN) AF: 0.0415 AC: 2214 AN: 53342

Middle Eastern (MID) AF: 0.0418 AC: 166 AN: 3970

European-Non Finnish (NFE) AF: 0.0708 AC: 71318 AN: 1007606

Other (OTH) AF: 0.0718 AC: 4043 AN: 56302

GnomAD4 genome AF: 0.0892 AC: 13578 AN: 152214 Hom.: 753 Cov.: 32 AF XY: 0.0878 AC XY: 6534 AN XY: 74428

African (AFR) AF: 0.146 AC: 6065 AN: 41508

American (AMR) AF: 0.0601 AC: 920 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0605 AC: 210 AN: 3472

East Asian (EAS) AF: 0.0985 AC: 510 AN: 5176

South Asian (SAS) AF: 0.0729 AC: 352 AN: 4828

European-Finnish (FIN) AF: 0.0457 AC: 485 AN: 10606

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0689 AC: 4684 AN: 68010

Other (OTH) AF: 0.0948 AC: 200 AN: 2110

Alfa AF: 0.0817 Hom.: 106

Bravo AF: 0.0943

Asia WGS AF: 0.100 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	6.9
DANN	Benign	0.87
PhyloP100		5.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10450321; hg19: chr10-37626859;