rs353810

Positions:

• chr9-86414276-A-C
• chr9-86414276-A-T

Variant summary

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

The ENST00000438582.2(ENSG00000235819):​n.32A>C 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 0.158 in 152,226 control chromosomes in the GnomAD database, including 2,066 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 0.16 (2066 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000235819 ENST00000438582.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

Genes affected

ENSG00000235819 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724080	XR_001746546.1	n.436A>C		non_coding_transcript_exon_variant	1/4
LOC102724080	XR_007061635.1	n.436A>C		non_coding_transcript_exon_variant	1/2
LOC102724080	XR_007061636.1	n.436A>C		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000235819	ENST00000438582.2	n.32A>C		non_coding_transcript_exon_variant	1/4	5
ENSG00000235819	ENST00000657061.1	n.64A>C		non_coding_transcript_exon_variant	1/2
ENSG00000235819	ENST00000660690.1	n.76A>C		non_coding_transcript_exon_variant	1/2
ENSG00000235819	ENST00000665072.1	n.57A>C		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24091 AN: 152108 Hom.: 2060 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0474

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.148

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.158 AC: 24116 AN: 152226 Hom.: 2066 Cov.: 32 AF XY: 0.160 AC XY: 11935 AN XY: 74444

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0473

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.150

Alfa AF: 0.135 Hom.: 378

Bravo AF: 0.152

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs353810; hg19: chr9-89029191;