rs7196352

Variant names:

• chr16-76854379-G-A
• rs7196352
• ENST00000567777.1:n.139-57976G>A

Variant summary

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

The ENST00000567777.1(ENSG00000259995):​n.139-57976G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,902 control chromosomes in the GnomAD database, including 15,646 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 0.45 (15646 hom., cov: 32)
• Consequence: ENSG00000259995 ENST00000567777.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646

Genes affected

ENSG00000259995 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 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
ENSG00000259995	ENST00000567777.1	n.139-57976G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67574 AN: 151784 Hom.: 15622 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.445 AC: 67655 AN: 151902 Hom.: 15646 Cov.: 32 AF XY: 0.445 AC XY: 33023 AN XY: 74256

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.428

Alfa AF: 0.436 Hom.: 2281

Bravo AF: 0.460

Asia WGS AF: 0.307 AC: 1067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7196352; hg19: chr16-76888276;