rs353810

Variant names:

• chr9-86414276-A-C
• rs353810
• ENST00000438582.2:n.32A>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000235819 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC102724080	XR_001746546.1	n.436A>C		non_coding_transcript_exon_variant	Exon 1 of 4
LOC102724080	XR_007061635.1	n.436A>C		non_coding_transcript_exon_variant	Exon 1 of 2
LOC102724080	XR_007061636.1	n.436A>C		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235819	ENST00000438582.2	n.32A>C		non_coding_transcript_exon_variant	Exon 1 of 4	5
ENSG00000235819	ENST00000657061.1	n.64A>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000235819	ENST00000660690.1	n.76A>C		non_coding_transcript_exon_variant	Exon 1 of 2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.101 AC: 4184 AN: 41546

American (AMR) AF: 0.193 AC: 2951 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3470

East Asian (EAS) AF: 0.0473 AC: 245 AN: 5180

South Asian (SAS) AF: 0.188 AC: 908 AN: 4826

European-Finnish (FIN) AF: 0.183 AC: 1941 AN: 10606

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12848 AN: 67984

Other (OTH) AF: 0.150 AC: 317 AN: 2116

Alfa AF: 0.146 Hom.: 727

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
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs353810; hg19: chr9-89029191;