5-141775016-C-T

Variant names:

• chr5-141775016-C-T
• rs193730
• ENST00000653358.1:n.172G>A

Variant summary

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

The ENST00000653358.1(ENSG00000286736):​n.172G>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 0.928 in 152,308 control chromosomes in the GnomAD database, including 65,669 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 0.93 (65669 hom., cov: 33)
• Consequence: ENSG00000286736 ENST00000653358.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371
• Publications: 2 publications found

Genes affected

ENSG00000286736 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901094	XR_007058975.1	n.206G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286736	ENST00000653358.1	n.172G>A		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000286736	ENST00000732556.1	n.167G>A		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000286736	ENST00000732555.1	n.135+19023G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.928 AC: 141267 AN: 152190 Hom.: 65617 Cov.: 33

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.869

Gnomad NFE AF: 0.919

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.928 AC: 141378 AN: 152308 Hom.: 65669 Cov.: 33 AF XY: 0.928 AC XY: 69099 AN XY: 74478

African (AFR) AF: 0.939 AC: 39010 AN: 41558

American (AMR) AF: 0.933 AC: 14288 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.933 AC: 3241 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5168 AN: 5176

South Asian (SAS) AF: 0.887 AC: 4283 AN: 4828

European-Finnish (FIN) AF: 0.931 AC: 9875 AN: 10612

Middle Eastern (MID) AF: 0.866 AC: 253 AN: 292

European-Non Finnish (NFE) AF: 0.919 AC: 62551 AN: 68036

Other (OTH) AF: 0.922 AC: 1951 AN: 2116

Alfa AF: 0.928 Hom.: 23548

Bravo AF: 0.932

Asia WGS AF: 0.950 AC: 3306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.90
DANN	Benign	0.39
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs193730; hg19: chr5-141154583;