rs7210837

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000283033 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000283033	ENST00000635352.1	n.519G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.100

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.191

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7210837; hg19: chr17-16764978;