rs9806234

chr15-74370692-A-Gchr15-74370692-A-T

Variant summary

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

The ENST00000568496.2(ENSG00000261821):n.4427A>G 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 0.407 in 152,072 control chromosomes in the GnomAD database, including 15,534 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 0.41 (15532 hom., cov: 32)
  • Exomes 𝑓: 0.50 (2 hom.)
• Consequence: ENST00000568496.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903524	XR_007064709.1	n.5075A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000568496.2	n.4427A>G		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61819 AN: 151942 Hom.: 15496 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.384

GnomAD4 exome AF: 0.500 AC: 6 AN: 12 Hom.: 2 Cov.: 0 AF XY: 0.833 AC XY: 5 AN XY: 6

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.407 AC: 61922 AN: 152060 Hom.: 15532 Cov.: 32 AF XY: 0.412 AC XY: 30591 AN XY: 74324

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.388

Alfa AF: 0.292 Hom.: 6966

Bravo AF: 0.422

Asia WGS AF: 0.639 AC: 2222 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	0.46
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9806234; hg19: chr15-74663033;