chr16-80902630-T-C

Variant names:

• chr16-80902630-T-C
• rs12446361
• ENST00000650780.1:c.82-71873A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650780.1(ENSG00000286221):​c.82-71873A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,112 control chromosomes in the GnomAD database, including 10,865 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 0.33 (10865 hom., cov: 33)
• Consequence: ENSG00000286221 ENST00000650780.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561
• Publications: 3 publications found

Genes affected

ENSG00000286221 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286221	ENST00000650780.1	c.82-71873A>G		intron_variant	Intron 2 of 2			ENSP00000498782.1

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50568 AN: 151994 Hom.: 10824 Cov.: 33

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.333 AC: 50666 AN: 152112 Hom.: 10865 Cov.: 33 AF XY: 0.331 AC XY: 24591 AN XY: 74378

African (AFR) AF: 0.613 AC: 25410 AN: 41466

American (AMR) AF: 0.299 AC: 4574 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 873 AN: 3470

East Asian (EAS) AF: 0.192 AC: 994 AN: 5164

South Asian (SAS) AF: 0.161 AC: 774 AN: 4820

European-Finnish (FIN) AF: 0.235 AC: 2487 AN: 10600

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14718 AN: 67990

Other (OTH) AF: 0.306 AC: 644 AN: 2106

Alfa AF: 0.267 Hom.: 17615

Bravo AF: 0.357

Asia WGS AF: 0.224 AC: 780 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	2.7
DANN	Benign	0.49
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs12446361; hg19: chr16-80936527;