16-82102961-C-T

Position:

• chr16-82102961-C-T

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 0.795 in 152,088 control chromosomes in the GnomAD database, including 49,060 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 0.79 (49060 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.82102961C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HSD17B2-AS1	ENST00000567021.1	n.44-31772G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120773 AN: 151970 Hom.: 49025 Cov.: 31

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.795 AC: 120857 AN: 152088 Hom.: 49060 Cov.: 31 AF XY: 0.790 AC XY: 58733 AN XY: 74334

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.861

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.807

Alfa AF: 0.855 Hom.: 32842

Bravo AF: 0.777

Asia WGS AF: 0.672 AC: 2340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3887358; hg19: chr16-82136566;