chr4-153966452-A-G

Position:

• chr4-153966452-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000660197.1(ENSG00000280241):​n.144+17591A>G variant causes a intron, non coding transcript 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: ENST00000660197.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC101927947	XR_007058336.1	n.3811-779A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000660197.1	n.144+17591A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.483

Alfa AF: 0.462 Hom.: 34251

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1878449; hg19: chr4-154887604;