5-41587464-A-T

Variant names:

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

Variant summary

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

The ENST00000504215.1(ENSG00000251478):​n.324T>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 0.0925 in 636,414 control chromosomes in the GnomAD database, including 3,964 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 (965 hom., cov: 33)
  • Exomes 𝑓: 0.089 (2999 hom.)
• Consequence: ENSG00000251478 ENST00000504215.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 3 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=-0.63).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15675 AN: 152136 Hom.: 963 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0846

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.00405

Gnomad SAS AF: 0.0635

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.111

GnomAD4 exome AF: 0.0892 AC: 43165 AN: 484160 Hom.: 2999 Cov.: 0 AF XY: 0.0885 AC XY: 23711 AN XY: 268030

African (AFR) AF: 0.201 AC: 2855 AN: 14226

American (AMR) AF: 0.0831 AC: 3196 AN: 38438

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 2182 AN: 15836

East Asian (EAS) AF: 0.00702 AC: 141 AN: 20088

South Asian (SAS) AF: 0.0794 AC: 5220 AN: 65748

European-Finnish (FIN) AF: 0.0583 AC: 2431 AN: 41722

Middle Eastern (MID) AF: 0.138 AC: 252 AN: 1830

European-Non Finnish (NFE) AF: 0.0931 AC: 24386 AN: 261998

Other (OTH) AF: 0.103 AC: 2502 AN: 24274

GnomAD4 genome AF: 0.103 AC: 15678 AN: 152254 Hom.: 965 Cov.: 33 AF XY: 0.100 AC XY: 7460 AN XY: 74452

African (AFR) AF: 0.178 AC: 7381 AN: 41526

American (AMR) AF: 0.0843 AC: 1290 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 418 AN: 3468

East Asian (EAS) AF: 0.00406 AC: 21 AN: 5168

South Asian (SAS) AF: 0.0627 AC: 303 AN: 4832

European-Finnish (FIN) AF: 0.0470 AC: 499 AN: 10616

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

European-Non Finnish (NFE) AF: 0.0802 AC: 5459 AN: 68028

Other (OTH) AF: 0.109 AC: 231 AN: 2112

Alfa AF: 0.100 Hom.: 111

Bravo AF: 0.110

Asia WGS AF: 0.0500 AC: 174 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	1.5
DANN	Benign	0.77
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs599176; hg19: chr5-41587566;