rs7210837

chr17-16861664-G-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: ENST00000635352.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000635352.1	n.519G>A		non_coding_transcript_exon_variant	1/1

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

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;