chr6-9450964-T-A

Variant names:

• chr6-9450964-T-A
• rs10484246

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 0.153 in 152,148 control chromosomes in the GnomAD database, including 2,129 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 0.15 (2129 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 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: 0.153 AC: 23260 AN: 152030 Hom.: 2122 Cov.: 32

Gnomad AFR AF: 0.0932

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0533

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.153 AC: 23281 AN: 152148 Hom.: 2129 Cov.: 32 AF XY: 0.152 AC XY: 11285 AN XY: 74394

Gnomad4 AFR AF: 0.0932

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0533

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.190

Alfa AF: 0.180 Hom.: 1497

Bravo AF: 0.162

Asia WGS AF: 0.253 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.25
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484246; hg19: chr6-9451197;