rs7196352

chr16-76854379-G-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, non coding transcript 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: ENST00000567777.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000567777.1	n.139-57976G>A		intron_variant, non_coding_transcript_variant		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;