9-2210993-C-T

Variant names:

• chr9-2210993-C-T
• rs7863990
• ENST00000816098.1:n.291+19588G>A

Variant summary

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

The ENST00000816098.1(ENSG00000306181):​n.291+19588G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,020 control chromosomes in the GnomAD database, including 6,670 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 0.28 (6670 hom., cov: 32)
• Consequence: ENSG00000306181 ENST00000816098.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816098.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306181	ENST00000816098.1		n.291+19588G>A		intron	N/A
	ENSG00000306181	ENST00000816099.1		n.295+19588G>A		intron	N/A
	ENSG00000306181	ENST00000816100.1		n.272+19588G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42699 AN: 151902 Hom.: 6659 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.0800

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.281 AC: 42733 AN: 152020 Hom.: 6670 Cov.: 32 AF XY: 0.277 AC XY: 20585 AN XY: 74322

African (AFR) AF: 0.422 AC: 17502 AN: 41454

American (AMR) AF: 0.272 AC: 4151 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 976 AN: 3470

East Asian (EAS) AF: 0.0802 AC: 414 AN: 5160

South Asian (SAS) AF: 0.260 AC: 1252 AN: 4814

European-Finnish (FIN) AF: 0.161 AC: 1701 AN: 10572

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15911 AN: 67984

Other (OTH) AF: 0.284 AC: 597 AN: 2100

Alfa AF: 0.253 Hom.: 6522

Bravo AF: 0.297

Asia WGS AF: 0.198 AC: 692 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.4
DANN	Benign	0.61
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs7863990; hg19: chr9-2210993; COSMIC: COSV69442477;