chr5-41587183-G-A

Variant names:

• chr5-41587183-G-A
• rs650073
• ENST00000504215.1:n.605C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000504215.1(ENSG00000251478):​n.605C>T 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 0.00127 in 244,326 control chromosomes in the GnomAD database, including 1 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 0.0018 (1 hom., cov: 33)
  • Exomes 𝑓: 0.00031 (0 hom.)
• Consequence: ENSG00000251478 ENST00000504215.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 4 publications found

Genes affected

ENSG00000251478 (HGNC:):

TCP1P2 (HGNC:11660):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251478	ENST00000504215.1	TSL:6	n.605C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000296840	ENST00000742936.1		n.105-358G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00184 AC: 280 AN: 152080 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.00640

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000524

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00143

GnomAD4 exome AF: 0.000315 AC: 29 AN: 92128 Hom.: 0 Cov.: 0 AF XY: 0.000179 AC XY: 9 AN XY: 50278

African (AFR) AF: 0.00926 AC: 19 AN: 2052

American (AMR) AF: 0.000359 AC: 3 AN: 8364

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1974

East Asian (EAS) AF: 0.00 AC: 0 AN: 3582

South Asian (SAS) AF: 0.00 AC: 0 AN: 10470

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6242

Middle Eastern (MID) AF: 0.00427 AC: 7 AN: 1640

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 53234

Other (OTH) AF: 0.00 AC: 0 AN: 4570

GnomAD4 genome AF: 0.00185 AC: 281 AN: 152198 Hom.: 1 Cov.: 33 AF XY: 0.00187 AC XY: 139 AN XY: 74410

African (AFR) AF: 0.00641 AC: 266 AN: 41522

American (AMR) AF: 0.000523 AC: 8 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5160

South Asian (SAS) AF: 0.00 AC: 0 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10602

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0000441 AC: 3 AN: 68014

Other (OTH) AF: 0.00142 AC: 3 AN: 2114

Alfa AF: 0.00 Hom.: 80

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.0
DANN	Benign	0.34
PhyloP100		0.0020

Splicing

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

Other links and lift over

dbSNP: rs650073; hg19: chr5-41587285;