chr4-153966452-A-G

Variant names:

• chr4-153966452-A-G
• rs1878449
• ENST00000660197.1:n.144+17591A>G

Variant summary

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

The ENST00000660197.1(ENSG00000280241):​n.144+17591A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 152,038 control chromosomes in the GnomAD database, including 20,141 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 0.51 (20141 hom., cov: 33)
• Consequence: ENSG00000280241 ENST00000660197.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527
• Publications: 5 publications found

Genes affected

ENSG00000280241 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927947	XR_007058336.1	n.3811-779A>G		intron_variant	Intron 7 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000280241	ENST00000660197.1	n.144+17591A>G		intron_variant	Intron 1 of 4
ENSG00000280241	ENST00000839747.1	n.664+17591A>G		intron_variant	Intron 6 of 8
ENSG00000280241	ENST00000839748.1	n.734+14307A>G		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77352 AN: 151920 Hom.: 20103 Cov.: 33

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.509 AC: 77444 AN: 152038 Hom.: 20141 Cov.: 33 AF XY: 0.513 AC XY: 38108 AN XY: 74288

African (AFR) AF: 0.587 AC: 24345 AN: 41470

American (AMR) AF: 0.535 AC: 8171 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1706 AN: 3468

East Asian (EAS) AF: 0.693 AC: 3588 AN: 5180

South Asian (SAS) AF: 0.556 AC: 2675 AN: 4814

European-Finnish (FIN) AF: 0.460 AC: 4853 AN: 10552

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30510 AN: 67970

Other (OTH) AF: 0.483 AC: 1021 AN: 2112

Alfa AF: 0.471 Hom.: 55286

Bravo AF: 0.521

Asia WGS AF: 0.630 AC: 2188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	13
DANN	Benign	0.85
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1878449; hg19: chr4-154887604;