chr9-95748856-T-C

Variant names:

• chr9-95748856-T-C
• rs700965

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 0.612 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.612 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

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.635

Alfa AF: 0.588 Hom.: 4740

Bravo AF: 0.591

Asia WGS AF: 0.763 AC: 2655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs700965; hg19: chr9-98511138;