chr5-88367793-C-A

Variant names:

• chr5-88367793-C-A
• rs10514299
• ENST00000501715.6:n.578-42280C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000501715.6(TMEM161B-DT):​n.578-42280C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: TMEM161B-DT ENST00000501715.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365
• Publications: 22 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM161B-DT	NR_039993.1	n.207-42280C>A		intron_variant	Intron 2 of 3
TMEM161B-DT	NR_039994.2	n.165-42280C>A		intron_variant	Intron 2 of 3
TMEM161B-DT	NR_039995.1	n.207-68480C>A		intron_variant	Intron 2 of 2
TMEM161B-DT	NR_105019.1	n.586-42280C>A		intron_variant	Intron 6 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM161B-DT	ENST00000501715.6	n.578-42280C>A		intron_variant	Intron 6 of 7	1
TMEM161B-DT	ENST00000501869.7	n.198-42280C>A		intron_variant	Intron 2 of 4	1
TMEM161B-DT	ENST00000504922.8	n.246-68480C>A		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 17475

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.74
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs10514299; hg19: chr5-87663610;