rs9332436

Variant names:

• chr8-48696059-G-A
• rs9332436
• ENST00000654201.1:n.271G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654201.1(ENSG00000253608):​n.271G>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 0.567 in 152,156 control chromosomes in the GnomAD database, including 28,668 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 0.57 (28668 hom., cov: 33)
• Consequence: ENSG00000253608 ENST00000654201.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.525
• Publications: 4 publications found

Genes affected

ENSG00000253608 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929268	NR_105002.1	n.420-499G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253608	ENST00000654201.1	n.271G>A		non_coding_transcript_exon_variant	Exon 4 of 5
ENSG00000253608	ENST00000741111.1	n.290G>A		non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000253608	ENST00000522575.1	n.420-499G>A		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86260 AN: 152038 Hom.: 28675 Cov.: 33

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.567 AC: 86272 AN: 152156 Hom.: 28668 Cov.: 33 AF XY: 0.574 AC XY: 42682 AN XY: 74380

African (AFR) AF: 0.197 AC: 8184 AN: 41518

American (AMR) AF: 0.605 AC: 9253 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2274 AN: 3470

East Asian (EAS) AF: 0.636 AC: 3281 AN: 5162

South Asian (SAS) AF: 0.592 AC: 2855 AN: 4824

European-Finnish (FIN) AF: 0.810 AC: 8580 AN: 10594

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.732 AC: 49763 AN: 67980

Other (OTH) AF: 0.588 AC: 1241 AN: 2110

Alfa AF: 0.632 Hom.: 4125

Bravo AF: 0.537

Asia WGS AF: 0.569 AC: 1977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.7
DANN	Benign	0.24
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs9332436; hg19: chr8-49608618;