rs8049365

Positions:

• chr16-76785421-C-T

Variant summary

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

The ENST00000567777.1(ENSG00000259995):​n.138+48942C>T 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 0.348 in 152,042 control chromosomes in the GnomAD database, including 9,492 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 0.35 (9492 hom., cov: 33)
• Consequence: ENST00000567777.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.395 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+48942C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52935 AN: 151926 Hom.: 9475 Cov.: 33

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.348 AC: 52985 AN: 152042 Hom.: 9492 Cov.: 33 AF XY: 0.349 AC XY: 25954 AN XY: 74314

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.352

Alfa AF: 0.342 Hom.: 1530

Bravo AF: 0.357

Asia WGS AF: 0.374 AC: 1300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.88
DANN	Benign	0.74

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: rs8049365; hg19: chr16-76819318;