9-7195408-A-G

Variant names:

• chr9-7195408-A-G
• rs2820914
• ENST00000649299.1:n.591-7326A>G

Variant summary

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

The ENST00000649299.1(ENSG00000285688):​n.591-7326A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,170 control chromosomes in the GnomAD database, including 5,045 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 0.26 (5045 hom., cov: 33)
• Consequence: ENSG00000285688 ENST00000649299.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 6 publications found

Genes affected

ENSG00000285688 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 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
ENSG00000285688	ENST00000649299.1	n.591-7326A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38811 AN: 152052 Hom.: 5048 Cov.: 33

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.255 AC: 38819 AN: 152170 Hom.: 5045 Cov.: 33 AF XY: 0.253 AC XY: 18802 AN XY: 74400

African (AFR) AF: 0.308 AC: 12786 AN: 41498

American (AMR) AF: 0.208 AC: 3188 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3470

East Asian (EAS) AF: 0.193 AC: 999 AN: 5180

South Asian (SAS) AF: 0.272 AC: 1311 AN: 4822

European-Finnish (FIN) AF: 0.224 AC: 2375 AN: 10592

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16152 AN: 67996

Other (OTH) AF: 0.276 AC: 583 AN: 2110

Alfa AF: 0.248 Hom.: 14852

Bravo AF: 0.256

Asia WGS AF: 0.218 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.4
DANN	Benign	0.85
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs2820914; hg19: chr9-7195408;