chr16-62045298-A-G

Variant names:

• chr16-62045298-A-G
• rs7498886
• ENST00000798664.1:n.245+8771A>G

Variant summary

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

The ENST00000798664.1(ENSG00000303989):​n.245+8771A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,694 control chromosomes in the GnomAD database, including 26,542 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 0.56 (26542 hom., cov: 30)
• Consequence: ENSG00000303989 ENST00000798664.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 5 publications found

Genes affected

ENSG00000303989 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798664.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303989	ENST00000798664.1		n.245+8771A>G		intron	N/A
	ENSG00000303989	ENST00000798665.1		n.184+8521A>G		intron	N/A
	ENSG00000303989	ENST00000798666.1		n.288+7955A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84860 AN: 151576 Hom.: 26491 Cov.: 30

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.603

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.560 AC: 84964 AN: 151694 Hom.: 26542 Cov.: 30 AF XY: 0.554 AC XY: 41062 AN XY: 74080

African (AFR) AF: 0.857 AC: 35496 AN: 41428

American (AMR) AF: 0.458 AC: 6988 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2001 AN: 3466

East Asian (EAS) AF: 0.345 AC: 1759 AN: 5104

South Asian (SAS) AF: 0.391 AC: 1871 AN: 4780

European-Finnish (FIN) AF: 0.467 AC: 4904 AN: 10500

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.446 AC: 30298 AN: 67872

Other (OTH) AF: 0.528 AC: 1110 AN: 2104

Alfa AF: 0.528 Hom.: 18932

Bravo AF: 0.575

Asia WGS AF: 0.434 AC: 1512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.046
DANN	Benign	0.31
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7498886; hg19: chr16-62079202;