4-52261891-G-A

Position:

• chr4-52261891-G-A

Variant summary

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

The ENST00000660768.1(ENSG00000287999):​n.204-8547C>T 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 0.731 in 151,968 control chromosomes in the GnomAD database, including 41,388 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 0.73 (41388 hom., cov: 32)
• Consequence: ENST00000660768.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000660768.1	n.204-8547C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111014 AN: 151850 Hom.: 41358 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.731 AC: 111098 AN: 151968 Hom.: 41388 Cov.: 32 AF XY: 0.733 AC XY: 54466 AN XY: 74284

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.815

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.915

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.784

Gnomad4 OTH AF: 0.766

Alfa AF: 0.760 Hom.: 7482

Bravo AF: 0.728

Asia WGS AF: 0.829 AC: 2884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1482108; hg19: chr4-53128057;