rs10450321

chr10-37337931-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00993	NR_104061.1	n.314-4395T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM161BP1	ENST00000457388.1	n.517T>C		non_coding_transcript_exon_variant	1/1
	ENST00000426471.6	n.315-4395T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000435629.5	n.204-4395T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000606476.1	n.158-4395T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR exome AF: 0.150

Gnomad4 AMR exome AF: 0.0647

Gnomad4 ASJ exome AF: 0.0662

Gnomad4 EAS exome AF: 0.0941

Gnomad4 SAS exome AF: 0.0655

Gnomad4 FIN exome AF: 0.0415

Gnomad4 NFE exome AF: 0.0708

Gnomad4 OTH exome AF: 0.0718

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

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.0601

Gnomad4 ASJ AF: 0.0605

Gnomad4 EAS AF: 0.0985

Gnomad4 SAS AF: 0.0729

Gnomad4 FIN AF: 0.0457

Gnomad4 NFE AF: 0.0689

Gnomad4 OTH AF: 0.0948

Alfa AF: 0.0797 Hom.: 97

Bravo AF: 0.0943

Asia WGS AF: 0.100 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
Cadd	Benign	6.9
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10450321; hg19: chr10-37626859;