9-95748856-T-C

Variant names:

• chr9-95748856-T-C
• rs700965

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 0.612 in 152,116 control chromosomes in the GnomAD database, including 29,820 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 0.61 (29820 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.612 AC: 93050 AN: 151998 Hom.: 29818 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.612 AC: 93080 AN: 152116 Hom.: 29820 Cov.: 32 AF XY: 0.621 AC XY: 46213 AN XY: 74372

African (AFR) AF: 0.406 AC: 16838 AN: 41462

American (AMR) AF: 0.649 AC: 9917 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2400 AN: 3468

East Asian (EAS) AF: 0.836 AC: 4337 AN: 5188

South Asian (SAS) AF: 0.717 AC: 3454 AN: 4820

European-Finnish (FIN) AF: 0.742 AC: 7858 AN: 10594

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46074 AN: 67976

Other (OTH) AF: 0.635 AC: 1341 AN: 2112

Alfa AF: 0.621 Hom.: 10354

Bravo AF: 0.591

Asia WGS AF: 0.763 AC: 2655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.30
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs700965; hg19: chr9-98511138;