9-97860315-T-C

Variant names:

• chr9-97860315-T-C
• rs907580

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 0.816 in 152,250 control chromosomes in the GnomAD database, including 51,395 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 0.82 (51395 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.816 AC: 124087 AN: 152132 Hom.: 51336 Cov.: 33

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.816 AC: 124199 AN: 152250 Hom.: 51395 Cov.: 33 AF XY: 0.823 AC XY: 61242 AN XY: 74436

African (AFR) AF: 0.940 AC: 39045 AN: 41552

American (AMR) AF: 0.818 AC: 12509 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2652 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5146 AN: 5178

South Asian (SAS) AF: 0.801 AC: 3862 AN: 4824

European-Finnish (FIN) AF: 0.833 AC: 8827 AN: 10602

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.730 AC: 49660 AN: 68006

Other (OTH) AF: 0.820 AC: 1733 AN: 2114

Alfa AF: 0.754 Hom.: 22492

Bravo AF: 0.824

Asia WGS AF: 0.917 AC: 3189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	10
DANN	Benign	0.86
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs907580; hg19: chr9-100622597;