chr5-41586303-T-C

Variant names:

• chr5-41586303-T-C
• rs583442
• ENST00000504215.1:n.1141A>G

Variant summary

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

The ENST00000504215.1(ENSG00000251478):​n.1141A>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 0.389 in 506,432 control chromosomes in the GnomAD database, including 40,421 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 0.41 (13419 hom., cov: 32)
  • Exomes 𝑓: 0.38 (27002 hom.)
• Consequence: ENSG00000251478 ENST00000504215.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.04
• 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=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 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.1141A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000296840	ENST00000742936.1		n.105-1238T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62089 AN: 151862 Hom.: 13415 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.426

GnomAD4 exome AF: 0.380 AC: 134816 AN: 354452 Hom.: 27002 Cov.: 0 AF XY: 0.389 AC XY: 73460 AN XY: 188622

African (AFR) AF: 0.550 AC: 5726 AN: 10414

American (AMR) AF: 0.272 AC: 4133 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 5430 AN: 10652

East Asian (EAS) AF: 0.428 AC: 9593 AN: 22434

South Asian (SAS) AF: 0.509 AC: 20845 AN: 40972

European-Finnish (FIN) AF: 0.296 AC: 7259 AN: 24538

Middle Eastern (MID) AF: 0.507 AC: 747 AN: 1472

European-Non Finnish (NFE) AF: 0.351 AC: 73246 AN: 208824

Other (OTH) AF: 0.393 AC: 7837 AN: 19958

GnomAD4 genome AF: 0.409 AC: 62118 AN: 151980 Hom.: 13419 Cov.: 32 AF XY: 0.408 AC XY: 30281 AN XY: 74290

African (AFR) AF: 0.546 AC: 22634 AN: 41442

American (AMR) AF: 0.324 AC: 4944 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1678 AN: 3470

East Asian (EAS) AF: 0.449 AC: 2303 AN: 5134

South Asian (SAS) AF: 0.509 AC: 2448 AN: 4812

European-Finnish (FIN) AF: 0.278 AC: 2938 AN: 10580

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23672 AN: 67952

Other (OTH) AF: 0.423 AC: 891 AN: 2106

Alfa AF: 0.373 Hom.: 32781

Bravo AF: 0.415

Asia WGS AF: 0.497 AC: 1727 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	2.0
DANN	Benign	0.32
PhyloP100		2.0

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: rs583442;

hg19: chr5-41586405;