chr16-76764575-A-C

Position:

• chr16-76764575-A-C

Variant summary

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

The ENST00000567777.1(ENSG00000259995):​n.138+28096A>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 0.364 in 151,942 control chromosomes in the GnomAD database, including 10,458 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 0.36 (10458 hom., cov: 32)
• Consequence: ENST00000567777.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 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
	ENST00000567777.1	n.138+28096A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55308 AN: 151822 Hom.: 10441 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.364 AC: 55359 AN: 151942 Hom.: 10458 Cov.: 32 AF XY: 0.364 AC XY: 27061 AN XY: 74254

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.363

Alfa AF: 0.266 Hom.: 912

Bravo AF: 0.375

Asia WGS AF: 0.376 AC: 1310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.7
DANN	Benign	0.16

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4888543; hg19: chr16-76798472;