9-30085412-T-C

Variant names:

• chr9-30085412-T-C
• rs1361925

Variant summary

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

The variant allele was found at a frequency of 0.607 in 151,876 control chromosomes in the GnomAD database, including 28,269 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 0.61 (28269 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 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

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92101 AN: 151760 Hom.: 28252 Cov.: 31

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.628

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.607 AC: 92156 AN: 151876 Hom.: 28269 Cov.: 31 AF XY: 0.603 AC XY: 44805 AN XY: 74248

African (AFR) AF: 0.646 AC: 26763 AN: 41434

American (AMR) AF: 0.622 AC: 9479 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2248 AN: 3464

East Asian (EAS) AF: 0.453 AC: 2334 AN: 5150

South Asian (SAS) AF: 0.428 AC: 2059 AN: 4816

European-Finnish (FIN) AF: 0.587 AC: 6192 AN: 10552

Middle Eastern (MID) AF: 0.628 AC: 182 AN: 290

European-Non Finnish (NFE) AF: 0.607 AC: 41251 AN: 67908

Other (OTH) AF: 0.623 AC: 1311 AN: 2104

Alfa AF: 0.605 Hom.: 20669

Bravo AF: 0.614

Asia WGS AF: 0.422 AC: 1464 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.4
DANN	Benign	0.89
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs1361925; hg19: chr9-30085410;