rs4916908

Positions:

• chr5-88383235-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000514065.1(ENSG00000250306):​n.288T>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.567 in 153,178 control chromosomes in the GnomAD database, including 26,295 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 0.57 (26101 hom., cov: 31)
  • Exomes 𝑓: 0.54 (194 hom.)
• Consequence: ENST00000514065.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.63

Genes affected

(HGNC:):

TMEM161B-DT (HGNC:43839): (TMEM161B divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM161B-DT	NR_039993.1	n.207-26838T>C		intron_variant, non_coding_transcript_variant
TMEM161B-DT	NR_039994.2	n.165-26838T>C		intron_variant, non_coding_transcript_variant
TMEM161B-DT	NR_039995.1	n.207-53038T>C		intron_variant, non_coding_transcript_variant
TMEM161B-DT	NR_105019.1	n.586-26838T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000514065.1	n.288T>C		non_coding_transcript_exon_variant	1/1
TMEM161B-DT	ENST00000658478.2	n.206-26838T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86008 AN: 151836 Hom.: 26046 Cov.: 31

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.550

GnomAD4 exome AF: 0.536 AC: 656 AN: 1224 Hom.: 194 Cov.: 0 AF XY: 0.527 AC XY: 390 AN XY: 740

Gnomad4 AFR exome AF: 0.929

Gnomad4 AMR exome AF: 0.600

Gnomad4 ASJ exome AF: 0.750

Gnomad4 EAS exome AF: 0.409

Gnomad4 SAS exome AF: 0.708

Gnomad4 FIN exome AF: 0.483

Gnomad4 NFE exome AF: 0.513

Gnomad4 OTH exome AF: 0.525

GnomAD4 genome AF: 0.567 AC: 86122 AN: 151954 Hom.: 26101 Cov.: 31 AF XY: 0.565 AC XY: 41970 AN XY: 74254

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.552

Alfa AF: 0.502 Hom.: 18542

Bravo AF: 0.580

Asia WGS AF: 0.465 AC: 1618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	2.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4916908; hg19: chr5-87679052;