17-16861664-G-A

Variant names:

• chr17-16861664-G-A
• rs7210837
• ENST00000635352.1:n.519G>A

Variant summary

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

The ENST00000635352.1(ENSG00000283033):​n.519G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,064 control chromosomes in the GnomAD database, including 2,932 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 0.19 (2931 hom., cov: 31)
  • Exomes 𝑓: 0.17 (1 hom.)
• Consequence: ENSG00000283033 ENST00000635352.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 3 publications found

Genes affected

ENSG00000283033 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635352.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283033	ENST00000635352.1	TSL:6	n.519G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28867 AN: 151922 Hom.: 2929 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.184

GnomAD4 exome AF: 0.167 AC: 4 AN: 24 Hom.: 1 Cov.: 0 AF XY: 0.188 AC XY: 3 AN XY: 16

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.100 AC: 2 AN: 20

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.190 AC: 28910 AN: 152040 Hom.: 2931 Cov.: 31 AF XY: 0.195 AC XY: 14460 AN XY: 74318

African (AFR) AF: 0.148 AC: 6158 AN: 41482

American (AMR) AF: 0.226 AC: 3449 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3470

East Asian (EAS) AF: 0.317 AC: 1630 AN: 5142

South Asian (SAS) AF: 0.306 AC: 1472 AN: 4814

European-Finnish (FIN) AF: 0.206 AC: 2181 AN: 10592

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12733 AN: 67946

Other (OTH) AF: 0.191 AC: 402 AN: 2108

Alfa AF: 0.183 Hom.: 321

Bravo AF: 0.190

Asia WGS AF: 0.346 AC: 1203 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	1.4
DANN	Benign	0.31
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7210837; hg19: chr17-16764978;