16-23179929-A-G

Position:

• chr16-23179929-A-G

Variant summary

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

The ENST00000648673.1(ENSG00000285613):​n.313+1523T>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 0.781 in 152,162 control chromosomes in the GnomAD database, including 47,522 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 0.78 (47522 hom., cov: 32)
• Consequence: ENST00000648673.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 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
	ENST00000648673.1	n.313+1523T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118728 AN: 152044 Hom.: 47458 Cov.: 32

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.781 AC: 118842 AN: 152162 Hom.: 47522 Cov.: 32 AF XY: 0.785 AC XY: 58355 AN XY: 74376

Gnomad4 AFR AF: 0.938

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.898

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.763

Alfa AF: 0.730 Hom.: 9673

Bravo AF: 0.799

Asia WGS AF: 0.902 AC: 3140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.1
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4421986; hg19: chr16-23191250;