6-24116622-T-C

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 0.0414 in 98,652 control chromosomes in the GnomAD database, including 90 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 0.041 (90 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.534

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0884 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: 0.0415 AC: 4087 AN: 98554 Hom.: 90 Cov.: 33

Gnomad AFR AF: 0.0918

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0282

Gnomad ASJ AF: 0.00466

Gnomad EAS AF: 0.000306

Gnomad SAS AF: 0.000466

Gnomad FIN AF: 0.00649

Gnomad MID AF: 0.0225

Gnomad NFE AF: 0.0265

Gnomad OTH AF: 0.0398

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

GnomAD4 genome AF: 0.0414 AC: 4084 AN: 98652 Hom.: 90 Cov.: 33 AF XY: 0.0393 AC XY: 1849 AN XY: 47016

Gnomad4 AFR AF: 0.0914

Gnomad4 AMR AF: 0.0281

Gnomad4 ASJ AF: 0.00466

Gnomad4 EAS AF: 0.000307

Gnomad4 SAS AF: 0.000466

Gnomad4 FIN AF: 0.00649

Gnomad4 NFE AF: 0.0265

Gnomad4 OTH AF: 0.0394

Alfa AF: 0.00948 Hom.: 1

Bravo AF: 0.0291

Asia WGS AF: 0.00173 AC: 6 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.9
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484657; hg19: chr6-24116850;