5-41587183-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000504215.1(ENSG00000251478):​n.605C>A 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 0.1 in 244,222 control chromosomes in the GnomAD database, including 1,449 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 0.10 (964 hom., cov: 33)
  • Exomes 𝑓: 0.096 (485 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

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.605C>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000296840	ENST00000742936.1		n.105-358G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15663 AN: 152066 Hom.: 962 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.00406

Gnomad SAS AF: 0.0636

Gnomad FIN AF: 0.0469

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.111

GnomAD4 exome AF: 0.0958 AC: 8814 AN: 92038 Hom.: 485 Cov.: 0 AF XY: 0.0969 AC XY: 4866 AN XY: 50228

African (AFR) AF: 0.245 AC: 503 AN: 2050

American (AMR) AF: 0.0945 AC: 789 AN: 8350

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 274 AN: 1966

East Asian (EAS) AF: 0.00447 AC: 16 AN: 3582

South Asian (SAS) AF: 0.104 AC: 1087 AN: 10464

European-Finnish (FIN) AF: 0.0617 AC: 385 AN: 6238

Middle Eastern (MID) AF: 0.0981 AC: 161 AN: 1642

European-Non Finnish (NFE) AF: 0.0963 AC: 5122 AN: 53176

Other (OTH) AF: 0.104 AC: 477 AN: 4570

GnomAD4 genome AF: 0.103 AC: 15666 AN: 152184 Hom.: 964 Cov.: 33 AF XY: 0.100 AC XY: 7457 AN XY: 74404

African (AFR) AF: 0.178 AC: 7373 AN: 41514

American (AMR) AF: 0.0843 AC: 1289 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 418 AN: 3466

East Asian (EAS) AF: 0.00407 AC: 21 AN: 5160

South Asian (SAS) AF: 0.0629 AC: 303 AN: 4820

European-Finnish (FIN) AF: 0.0469 AC: 497 AN: 10600

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0803 AC: 5458 AN: 68010

Other (OTH) AF: 0.109 AC: 231 AN: 2114

Alfa AF: 0.0597 Hom.: 80

Bravo AF: 0.111

Asia WGS AF: 0.0500 AC: 174 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	0.93
DANN	Benign	0.40
PhyloP100		0.0020

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: rs650073;

hg19: chr5-41587285;