rs174643

Variant names:

• chr16-1083049-G-A
• rs174643
• ENST00000725498.1:n.466+60G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000725498.1(ENSG00000294721):​n.466+60G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 151,942 control chromosomes in the GnomAD database, including 22,291 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 0.53 (22291 hom., cov: 32)
• Consequence: ENSG00000294721 ENST00000725498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495
• Publications: 11 publications found

Genes affected

ENSG00000294721 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294721	ENST00000725498.1	n.466+60G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80845 AN: 151824 Hom.: 22279 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.532 AC: 80908 AN: 151942 Hom.: 22291 Cov.: 32 AF XY: 0.530 AC XY: 39385 AN XY: 74274

African (AFR) AF: 0.579 AC: 24002 AN: 41442

American (AMR) AF: 0.571 AC: 8728 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1353 AN: 3472

East Asian (EAS) AF: 0.122 AC: 628 AN: 5162

South Asian (SAS) AF: 0.331 AC: 1593 AN: 4814

European-Finnish (FIN) AF: 0.599 AC: 6335 AN: 10584

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36709 AN: 67868

Other (OTH) AF: 0.501 AC: 1059 AN: 2114

Alfa AF: 0.538 Hom.: 36825

Bravo AF: 0.538

Asia WGS AF: 0.258 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.1
DANN	Benign	0.83
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs174643; hg19: chr16-1133049;