rs146696563

Variant names:

• chr6-24062560-T-C
• rs146696563

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.00884 in 152,236 control chromosomes in the GnomAD database, including 10 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 0.0088 (10 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS2: High Homozygotes in GnomAd4 at 10 gene

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: 0.00884 AC: 1345 AN: 152118 Hom.: 10 Cov.: 31

Gnomad AFR AF: 0.00176

Gnomad AMI AF: 0.0209

Gnomad AMR AF: 0.00511

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.0199

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0132

Gnomad OTH AF: 0.0100

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

GnomAD4 genome AF: 0.00884 AC: 1346 AN: 152236 Hom.: 10 Cov.: 31 AF XY: 0.00846 AC XY: 630 AN XY: 74440

Gnomad4 AFR AF: 0.00176

Gnomad4 AMR AF: 0.00510

Gnomad4 ASJ AF: 0.00778

Gnomad4 EAS AF: 0.000967

Gnomad4 SAS AF: 0.00228

Gnomad4 FIN AF: 0.0199

Gnomad4 NFE AF: 0.0132

Gnomad4 OTH AF: 0.0104

Alfa AF: 0.0120 Hom.: 0

Bravo AF: 0.00747

Asia WGS AF: 0.00231 AC: 8 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs146696563; hg19: chr6-24062788;