5-29891908-T-C

Variant names:

• chr5-29891908-T-C
• rs4242135
• ENST00000720780.1:n.279-860T>C

Variant summary

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

The ENST00000720780.1(ENSG00000294076):​n.279-860T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.953 in 152,142 control chromosomes in the GnomAD database, including 69,178 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 0.95 (69178 hom., cov: 31)
• Consequence: ENSG00000294076 ENST00000720780.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.50
• Publications: 1 publications found

Genes affected

ENSG00000294076 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720780.1. 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
	ENSG00000294076	ENST00000720780.1		n.279-860T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.953 AC: 144870 AN: 152024 Hom.: 69128 Cov.: 31

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.969

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.953 AC: 144979 AN: 152142 Hom.: 69178 Cov.: 31 AF XY: 0.954 AC XY: 70935 AN XY: 74374

African (AFR) AF: 0.897 AC: 37243 AN: 41512

American (AMR) AF: 0.976 AC: 14884 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3288 AN: 3470

East Asian (EAS) AF: 0.977 AC: 5058 AN: 5176

South Asian (SAS) AF: 0.969 AC: 4679 AN: 4830

European-Finnish (FIN) AF: 0.988 AC: 10488 AN: 10614

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.973 AC: 66141 AN: 67970

Other (OTH) AF: 0.953 AC: 2008 AN: 2108

Alfa AF: 0.965 Hom.: 23651

Bravo AF: 0.950

Asia WGS AF: 0.973 AC: 3382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.20
PhyloP100		-3.5

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: rs4242135;

hg19: chr5-29892015;