rs993501

Variant names:

• chr9-97861095-G-A
• rs993501

Your query was ambiguous. Multiple possible variants found:

• chr9-97861095-G-A
• chr9-97861095-G-T

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 0.729 in 152,094 control chromosomes in the GnomAD database, including 41,743 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 0.73 (41743 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 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: 0.729 AC: 110734 AN: 151976 Hom.: 41690 Cov.: 31

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.729 AC: 110837 AN: 152094 Hom.: 41743 Cov.: 31 AF XY: 0.731 AC XY: 54375 AN XY: 74354

African (AFR) AF: 0.912 AC: 37865 AN: 41514

American (AMR) AF: 0.696 AC: 10637 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2211 AN: 3472

East Asian (EAS) AF: 0.986 AC: 5103 AN: 5178

South Asian (SAS) AF: 0.688 AC: 3323 AN: 4828

European-Finnish (FIN) AF: 0.648 AC: 6849 AN: 10570

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42739 AN: 67938

Other (OTH) AF: 0.718 AC: 1514 AN: 2110

Alfa AF: 0.704 Hom.: 9261

Bravo AF: 0.743

Asia WGS AF: 0.816 AC: 2839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.52
PhyloP100		0.093

Splicing

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

Other links and lift over

dbSNP: rs993501; hg19: chr9-100623377;