16-84924405-T-C

Variant names:

• chr16-84924405-T-C
• rs7189551
• ENST00000625056.2:n.152+252A>G

Variant summary

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

The ENST00000625056.2(ENSG00000279622):​n.152+252A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,054 control chromosomes in the GnomAD database, including 7,939 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 0.31 (7939 hom., cov: 34)
• Consequence: ENSG00000279622 ENST00000625056.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.965

Genes affected

ENSG00000279622 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 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
ENSG00000279622	ENST00000625056.2	n.152+252A>G		intron_variant	Intron 1 of 2	6

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46533 AN: 151936 Hom.: 7918 Cov.: 34

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.306 AC: 46602 AN: 152054 Hom.: 7939 Cov.: 34 AF XY: 0.305 AC XY: 22709 AN XY: 74352

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.297

Alfa AF: 0.122 Hom.: 196

Bravo AF: 0.318

Asia WGS AF: 0.220 AC: 765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7189551; hg19: chr16-84958011;