9-2273601-G-A

Variant names:

• chr9-2273601-G-A
• rs10123149
• ENST00000816240.1:n.346G>A

Variant summary

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

The ENST00000816240.1(ENSG00000306202):​n.346G>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 0.503 in 152,064 control chromosomes in the GnomAD database, including 20,442 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 0.50 (20442 hom., cov: 32)
• Consequence: ENSG00000306202 ENST00000816240.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485
• Publications: 0 publications found

Genes affected

ENSG00000306202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306202	ENST00000816240.1	n.346G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000306202	ENST00000816241.1	n.442G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000306202	ENST00000816244.1	n.373G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76448 AN: 151946 Hom.: 20421 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.503 AC: 76518 AN: 152064 Hom.: 20442 Cov.: 32 AF XY: 0.510 AC XY: 37916 AN XY: 74334

African (AFR) AF: 0.642 AC: 26629 AN: 41458

American (AMR) AF: 0.513 AC: 7836 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1542 AN: 3466

East Asian (EAS) AF: 0.870 AC: 4505 AN: 5178

South Asian (SAS) AF: 0.569 AC: 2745 AN: 4828

European-Finnish (FIN) AF: 0.451 AC: 4763 AN: 10564

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.395 AC: 26872 AN: 67976

Other (OTH) AF: 0.491 AC: 1036 AN: 2110

Alfa AF: 0.404 Hom.: 9096

Bravo AF: 0.515

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	1.9
DANN	Benign	0.70
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs10123149; hg19: chr9-2273601;