chr5-136000872-A-G

Variant names:

• chr5-136000872-A-G
• rs13157444
• ENST00000727979.1:n.429+490T>C

Variant summary

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

The ENST00000727979.1(ENSG00000295093):​n.429+490T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,810 control chromosomes in the GnomAD database, including 17,663 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 0.47 (17663 hom., cov: 31)
• Consequence: ENSG00000295093 ENST00000727979.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 8 publications found

Genes affected

ENSG00000295093 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295093	ENST00000727979.1	n.429+490T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.468 AC: 70955 AN: 151692 Hom.: 17639 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.417

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.468 AC: 71018 AN: 151810 Hom.: 17663 Cov.: 31 AF XY: 0.469 AC XY: 34762 AN XY: 74150

African (AFR) AF: 0.608 AC: 25121 AN: 41348

American (AMR) AF: 0.403 AC: 6146 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3464

East Asian (EAS) AF: 0.734 AC: 3766 AN: 5128

South Asian (SAS) AF: 0.470 AC: 2261 AN: 4814

European-Finnish (FIN) AF: 0.440 AC: 4629 AN: 10522

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.389 AC: 26454 AN: 67966

Other (OTH) AF: 0.417 AC: 878 AN: 2106

Alfa AF: 0.423 Hom.: 16274

Bravo AF: 0.476

Asia WGS AF: 0.579 AC: 2013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.39
DANN	Benign	0.55
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs13157444; hg19: chr5-135336561;