5-88206508-G-GA

Position:

• chr5-88206508-G-GA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_153354.5(TMEM161B):​c.599-10_599-9insT variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00799 in 1,300,318 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0033 (2 hom., cov: 32)
  • Exomes 𝑓: 0.0086 (0 hom.)
• Consequence: TMEM161B NM_153354.5 splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.544

Genes affected

TMEM161B (HGNC:28483): (transmembrane protein 161B) Predicted to enable nucleic acid binding activity. Predicted to be involved in DNA integration. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 5-88206508-G-GA is Benign according to our data. Variant chr5-88206508-G-GA is described in ClinVar as [Benign]. Clinvar id is 2798672.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.00859 (9888/1150926) while in subpopulation AFR AF= 0.0279 (717/25656). AF 95% confidence interval is 0.0263. There are 0 homozygotes in gnomad4_exome. There are 4948 alleles in male gnomad4_exome subpopulation. Median coverage is 28. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM161B	NM_153354.5	c.599-10_599-9insT		splice_polypyrimidine_tract_variant, intron_variant		ENST00000296595.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM161B	ENST00000296595.11	c.599-10_599-9insT		splice_polypyrimidine_tract_variant, intron_variant		1	NM_153354.5	P1

Frequencies

GnomAD3 genomes AF: 0.00334 AC: 498 AN: 149306 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.0106

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00267

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000195

Gnomad SAS AF: 0.000210

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000283

Gnomad OTH AF: 0.00343

GnomAD4 exome AF: 0.00859 AC: 9888 AN: 1150926 Hom.: 0 Cov.: 28 AF XY: 0.00867 AC XY: 4948 AN XY: 570702

Gnomad4 AFR exome AF: 0.0279

Gnomad4 AMR exome AF: 0.0145

Gnomad4 ASJ exome AF: 0.00644

Gnomad4 EAS exome AF: 0.0186

Gnomad4 SAS exome AF: 0.0110

Gnomad4 FIN exome AF: 0.00842

Gnomad4 NFE exome AF: 0.00735

Gnomad4 OTH exome AF: 0.00929

GnomAD4 genome AF: 0.00333 AC: 498 AN: 149392 Hom.: 2 Cov.: 32 AF XY: 0.00332 AC XY: 242 AN XY: 72870

Gnomad4 AFR AF: 0.0105

Gnomad4 AMR AF: 0.00267

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000196

Gnomad4 SAS AF: 0.000210

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000283

Gnomad4 OTH AF: 0.00340

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 17, 2024

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs558912554; hg19: chr5-87502325;