9-97864602-A-G

Variant names:

• chr9-97864602-A-G
• rs7860144

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.684

Alfa AF: 0.559 Hom.: 1778

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7860144; hg19: chr9-100626884;