rs598318

Variant names:

• chr5-41587260-T-C
• rs598318
• ENST00000504215.1:n.528A>G

Variant summary

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

The ENST00000504215.1(ENSG00000251478):​n.528A>G 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 0.173 in 412,810 control chromosomes in the GnomAD database, including 7,350 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 0.19 (3276 hom., cov: 33)
  • Exomes 𝑓: 0.16 (4074 hom.)
• Consequence: ENSG00000251478 ENST00000504215.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 2 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=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 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.528A>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000296840	ENST00000742936.1		n.105-281T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29070 AN: 152114 Hom.: 3271 Cov.: 33

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.00484

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0809

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.208

GnomAD4 exome AF: 0.162 AC: 42156 AN: 260578 Hom.: 4074 Cov.: 0 AF XY: 0.163 AC XY: 23760 AN XY: 145518

African (AFR) AF: 0.346 AC: 2497 AN: 7220

American (AMR) AF: 0.134 AC: 2511 AN: 18674

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1643 AN: 5650

East Asian (EAS) AF: 0.00371 AC: 44 AN: 11864

South Asian (SAS) AF: 0.161 AC: 7021 AN: 43720

European-Finnish (FIN) AF: 0.100 AC: 1615 AN: 16106

Middle Eastern (MID) AF: 0.255 AC: 574 AN: 2254

European-Non Finnish (NFE) AF: 0.169 AC: 24085 AN: 142870

Other (OTH) AF: 0.177 AC: 2166 AN: 12220

GnomAD4 genome AF: 0.191 AC: 29080 AN: 152232 Hom.: 3276 Cov.: 33 AF XY: 0.185 AC XY: 13802 AN XY: 74438

African (AFR) AF: 0.312 AC: 12951 AN: 41528

American (AMR) AF: 0.152 AC: 2325 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 969 AN: 3468

East Asian (EAS) AF: 0.00485 AC: 25 AN: 5156

South Asian (SAS) AF: 0.139 AC: 670 AN: 4826

European-Finnish (FIN) AF: 0.0809 AC: 859 AN: 10614

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10657 AN: 68014

Other (OTH) AF: 0.205 AC: 434 AN: 2116

Alfa AF: 0.173 Hom.: 1299

Bravo AF: 0.205

Asia WGS AF: 0.0910 AC: 316 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	2.8
DANN	Benign	0.56
PhyloP100		0.35

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: rs598318;

hg19: chr5-41587362;