5-88383235-T-C

Variant names:

• chr5-88383235-T-C
• rs4916908
• ENST00000501715.6:n.578-26838T>C

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000250306 ENST00000514065.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.63
• Publications: 5 publications found

Genes affected

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

ENSG00000250306 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514065.1. 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
	TMEM161B-DT	NR_039993.1		n.207-26838T>C		intron	N/A
	TMEM161B-DT	NR_039994.2		n.165-26838T>C		intron	N/A
	TMEM161B-DT	NR_039995.1		n.207-53038T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM161B-DT	ENST00000501715.6	TSL:1	n.578-26838T>C		intron	N/A
	TMEM161B-DT	ENST00000501869.7	TSL:1	n.198-26838T>C		intron	N/A
	ENSG00000250306	ENST00000514065.1	TSL:6	n.288T>C		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AF: 0.929 AC: 13 AN: 14

American (AMR) AF: 0.600 AC: 6 AN: 10

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 3 AN: 4

East Asian (EAS) AF: 0.409 AC: 9 AN: 22

South Asian (SAS) AF: 0.708 AC: 143 AN: 202

European-Finnish (FIN) AF: 0.483 AC: 226 AN: 468

Middle Eastern (MID) AF: 0.333 AC: 6 AN: 18

European-Non Finnish (NFE) AF: 0.513 AC: 229 AN: 446

Other (OTH) AF: 0.525 AC: 21 AN: 40

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

African (AFR) AF: 0.797 AC: 33044 AN: 41464

American (AMR) AF: 0.501 AC: 7640 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2267 AN: 3468

East Asian (EAS) AF: 0.374 AC: 1927 AN: 5154

South Asian (SAS) AF: 0.558 AC: 2690 AN: 4818

European-Finnish (FIN) AF: 0.475 AC: 5013 AN: 10544

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31770 AN: 67942

Other (OTH) AF: 0.552 AC: 1161 AN: 2102

Alfa AF: 0.514 Hom.: 25897

Bravo AF: 0.580

Asia WGS AF: 0.465 AC: 1618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	2.3
DANN	Benign	0.64
PhyloP100		3.6

Splicing

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

Other links and lift over

dbSNP: rs4916908; hg19: chr5-87679052; COSMIC: COSV107501603;