rs2166277

chr4-32639755-A-G

Variant summary

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

The ENST00000659320.1(ENSG00000286784):n.216-54459T>C 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 0.104 in 152,226 control chromosomes in the GnomAD database, including 2,051 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 0.10 (2051 hom., cov: 33)
• Consequence: ENST00000659320.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.94

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 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
	ENST00000659320.1	n.216-54459T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15837 AN: 152106 Hom.: 2049 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0718

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.0433

Gnomad FIN AF: 0.0282

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.00870

Gnomad OTH AF: 0.0761

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

GnomAD4 genome AF: 0.104 AC: 15864 AN: 152226 Hom.: 2051 Cov.: 33 AF XY: 0.103 AC XY: 7658 AN XY: 74416

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.0719

Gnomad4 ASJ AF: 0.00432

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.0427

Gnomad4 FIN AF: 0.0282

Gnomad4 NFE AF: 0.00870

Gnomad4 OTH AF: 0.0753

Alfa AF: 0.0638 Hom.: 143

Bravo AF: 0.118

Asia WGS AF: 0.145 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	9.7
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2166277; hg19: chr4-32641377;