chr20-17038329-G-A

Variant names:

• chr20-17038329-G-A
• rs16998603
• ENST00000835698.1:n.292-3485G>A

Variant summary

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

The ENST00000835698.1(ENSG00000308686):​n.292-3485G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 151,966 control chromosomes in the GnomAD database, including 1,487 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 0.14 (1487 hom., cov: 32)
• Consequence: ENSG00000308686 ENST00000835698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.652
• Publications: 2 publications found

Genes affected

ENSG00000308686 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835698.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308686	ENST00000835698.1		n.292-3485G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20781 AN: 151848 Hom.: 1485 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.137 AC: 20794 AN: 151966 Hom.: 1487 Cov.: 32 AF XY: 0.137 AC XY: 10155 AN XY: 74270

African (AFR) AF: 0.147 AC: 6117 AN: 41472

American (AMR) AF: 0.106 AC: 1611 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3468

East Asian (EAS) AF: 0.248 AC: 1272 AN: 5134

South Asian (SAS) AF: 0.201 AC: 966 AN: 4808

European-Finnish (FIN) AF: 0.137 AC: 1446 AN: 10584

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8350 AN: 67934

Other (OTH) AF: 0.133 AC: 281 AN: 2108

Alfa AF: 0.0848 Hom.: 132

Bravo AF: 0.133

Asia WGS AF: 0.205 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.3
DANN	Benign	0.58
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs16998603; hg19: chr20-17018974;