rs650073

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr5-41587183-G-A
• chr5-41587183-G-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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCP1P2		n.41587183G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251478	ENST00000504215.1	n.605C>T		non_coding_transcript_exon_variant	Exon 1 of 2	6
ENSG00000296840	ENST00000742936.1	n.105-358G>A		intron_variant	Intron 1 of 1

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 v4.3

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;