rs723751

chr1-169496759-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000392097.5(ENSG00000213062):n.10684G>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 0.272 in 151,964 control chromosomes in the GnomAD database, including 5,735 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 0.27 (5735 hom., cov: 31)
• Consequence: ENST00000392097.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.368 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
	ENST00000392097.5	n.10684G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41312 AN: 151846 Hom.: 5724 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.272 AC: 41339 AN: 151964 Hom.: 5735 Cov.: 31 AF XY: 0.272 AC XY: 20184 AN XY: 74276

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.258

Alfa AF: 0.267 Hom.: 7371

Bravo AF: 0.282

Asia WGS AF: 0.292 AC: 1015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.4
Dann	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs723751; hg19: chr1-169465997;