chr9-2212546-G-A

Variant names:

• chr9-2212546-G-A
• rs1535842
• ENST00000816098.1:n.291+18035C>T

Variant summary

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

The ENST00000816098.1(ENSG00000306181):​n.291+18035C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,020 control chromosomes in the GnomAD database, including 26,970 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 0.58 (26970 hom., cov: 32)
• Consequence: ENSG00000306181 ENST00000816098.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 3 publications found

Genes affected

ENSG00000306181 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987043	XR_001746600.2	n.297+18035C>T		intron_variant	Intron 2 of 3
LOC107987043	XR_007061395.1	n.301+18035C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306181	ENST00000816098.1	n.291+18035C>T		intron_variant	Intron 2 of 4
ENSG00000306181	ENST00000816099.1	n.295+18035C>T		intron_variant	Intron 2 of 3
ENSG00000306181	ENST00000816100.1	n.272+18035C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87826 AN: 151902 Hom.: 26947 Cov.: 32

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.578 AC: 87890 AN: 152020 Hom.: 26970 Cov.: 32 AF XY: 0.572 AC XY: 42519 AN XY: 74302

African (AFR) AF: 0.793 AC: 32901 AN: 41498

American (AMR) AF: 0.497 AC: 7593 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1889 AN: 3464

East Asian (EAS) AF: 0.466 AC: 2406 AN: 5166

South Asian (SAS) AF: 0.516 AC: 2483 AN: 4816

European-Finnish (FIN) AF: 0.450 AC: 4745 AN: 10546

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.503 AC: 34162 AN: 67930

Other (OTH) AF: 0.563 AC: 1187 AN: 2110

Alfa AF: 0.535 Hom.: 38804

Bravo AF: 0.593

Asia WGS AF: 0.488 AC: 1700 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.66
DANN	Benign	0.59
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1535842; hg19: chr9-2212546;