chr16-35281704-T-C

Position:

• chr16-35281704-T-C

Variant summary

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

The variant allele was found at a frequency of 0.755 in 152,020 control chromosomes in the GnomAD database, including 43,917 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 0.76 (43917 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.35281704T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000260958	ENST00000562572.1	n.86-2052T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114683 AN: 151902 Hom.: 43871 Cov.: 33

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.755 AC: 114785 AN: 152020 Hom.: 43917 Cov.: 33 AF XY: 0.749 AC XY: 55646 AN XY: 74290

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.761

Alfa AF: 0.787 Hom.: 106047

Bravo AF: 0.762

Asia WGS AF: 0.511 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7196505; hg19: chr16-34516075;