9-130256919-T-C

Variant names:

• chr9-130256919-T-C
• rs7045878

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 0.738 in 152,010 control chromosomes in the GnomAD database, including 41,796 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 0.74 (41796 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 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: 0.738 AC: 112077 AN: 151892 Hom.: 41745 Cov.: 30

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.738 AC: 112189 AN: 152010 Hom.: 41796 Cov.: 30 AF XY: 0.740 AC XY: 55013 AN XY: 74312

African (AFR) AF: 0.806 AC: 33419 AN: 41470

American (AMR) AF: 0.738 AC: 11264 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2015 AN: 3470

East Asian (EAS) AF: 0.988 AC: 5115 AN: 5178

South Asian (SAS) AF: 0.841 AC: 4048 AN: 4814

European-Finnish (FIN) AF: 0.685 AC: 7224 AN: 10544

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46803 AN: 67970

Other (OTH) AF: 0.719 AC: 1513 AN: 2104

Alfa AF: 0.696 Hom.: 51828

Bravo AF: 0.744

Asia WGS AF: 0.896 AC: 3119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	9.1
DANN	Benign	0.68
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs7045878; hg19: chr9-133019198; COSMIC: COSV60403319;