rs733140

Positions:

• chr16-55290182-A-G
• chr16-55290182-A-T

Variant summary

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

The ENST00000558730.2(ENSG00000259283):​n.89-7518T>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 0.266 in 152,074 control chromosomes in the GnomAD database, including 5,662 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 0.27 (5662 hom., cov: 32)
• Consequence: ENST00000558730.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000558730.2	n.89-7518T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40394 AN: 151956 Hom.: 5656 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.266 AC: 40410 AN: 152074 Hom.: 5662 Cov.: 32 AF XY: 0.264 AC XY: 19636 AN XY: 74330

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.243

Alfa AF: 0.244 Hom.: 2386

Bravo AF: 0.263

Asia WGS AF: 0.242 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	8.6
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs733140; hg19: chr16-55324094;