rs9495441

chr6-99759290-A-G

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 0.0994 in 151,992 control chromosomes in the GnomAD database, including 1,306 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 0.099 (1306 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.232

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0994 AC: 15091 AN: 151874 Hom.: 1304 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0582

Gnomad ASJ AF: 0.0615

Gnomad EAS AF: 0.00673

Gnomad SAS AF: 0.0654

Gnomad FIN AF: 0.0548

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0464

Gnomad OTH AF: 0.0842

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

GnomAD4 genome AF: 0.0994 AC: 15113 AN: 151992 Hom.: 1306 Cov.: 32 AF XY: 0.0980 AC XY: 7279 AN XY: 74308

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.0581

Gnomad4 ASJ AF: 0.0615

Gnomad4 EAS AF: 0.00675

Gnomad4 SAS AF: 0.0663

Gnomad4 FIN AF: 0.0548

Gnomad4 NFE AF: 0.0464

Gnomad4 OTH AF: 0.0833

Alfa AF: 0.0844 Hom.: 128

Bravo AF: 0.105

Asia WGS AF: 0.0540 AC: 186 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.9
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9495441; hg19: chr6-100207166;