chr9-97864602-A-G

Variant names:

• chr9-97864602-A-G
• rs7860144

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 0.682 in 152,102 control chromosomes in the GnomAD database, including 35,741 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 0.68 (35741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652
• Publications: 4 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 = 0.9 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: 0.682 AC: 103622 AN: 151984 Hom.: 35705 Cov.: 32

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.682 AC: 103702 AN: 152102 Hom.: 35741 Cov.: 32 AF XY: 0.685 AC XY: 50971 AN XY: 74374

African (AFR) AF: 0.760 AC: 31520 AN: 41490

American (AMR) AF: 0.680 AC: 10395 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2199 AN: 3466

East Asian (EAS) AF: 0.922 AC: 4772 AN: 5178

South Asian (SAS) AF: 0.673 AC: 3246 AN: 4820

European-Finnish (FIN) AF: 0.647 AC: 6838 AN: 10566

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42695 AN: 67974

Other (OTH) AF: 0.684 AC: 1445 AN: 2114

Alfa AF: 0.574 Hom.: 2004

Bravo AF: 0.690

Asia WGS AF: 0.780 AC: 2714 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	0.91
DANN	Benign	0.56
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs7860144; hg19: chr9-100626884;