rs599176

Variant names:

• chr5-41587464-A-G
• rs599176
• ENST00000504215.1:n.324T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-41587464-A-G
• chr5-41587464-A-T

Variant summary

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

The ENST00000504215.1(ENSG00000251478):​n.324T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000619 in 484,540 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 33)
  • Exomes 𝑓: 0.0000062 (0 hom.)
• Consequence: ENSG00000251478 ENST00000504215.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 0 publications found

Genes affected

ENSG00000251478 (HGNC:):

TCP1P2 (HGNC:11660):

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=-0.58).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504215.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251478	ENST00000504215.1	TSL:6	n.324T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000296840	ENST00000742936.1		n.105-77A>G		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000619 AC: 3 AN: 484540 Hom.: 0 Cov.: 0 AF XY: 0.00000746 AC XY: 2 AN XY: 268266

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 14232

American (AMR) AF: 0.00 AC: 0 AN: 38538

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15854

East Asian (EAS) AF: 0.0000498 AC: 1 AN: 20092

South Asian (SAS) AF: 0.00 AC: 0 AN: 65770

European-Finnish (FIN) AF: 0.0000240 AC: 1 AN: 41724

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1830

European-Non Finnish (NFE) AF: 0.00000381 AC: 1 AN: 262208

Other (OTH) AF: 0.00 AC: 0 AN: 24292

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0160444), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	1.8
DANN	Benign	0.79
PhyloP100		1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs599176;

hg19: chr5-41587566;