rs75560005

Positions:

• chr6-29636005-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 0.00629 in 1,478,756 control chromosomes in the GnomAD database, including 272 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 0.0060 (18 hom., cov: 32)
  • Exomes 𝑓: 0.0063 (254 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0631 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: 0.00598 AC: 911 AN: 152214 Hom.: 18 Cov.: 32

Gnomad AFR AF: 0.000700

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.00209

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.0693

Gnomad SAS AF: 0.0549

Gnomad FIN AF: 0.000942

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00263

Gnomad OTH AF: 0.00621

GnomAD4 exome AF: 0.00633 AC: 8396 AN: 1326424 Hom.: 254 AF XY: 0.00776 AC XY: 5172 AN XY: 666300

Gnomad4 AFR exome AF: 0.000587

Gnomad4 AMR exome AF: 0.00169

Gnomad4 ASJ exome AF: 0.00484

Gnomad4 EAS exome AF: 0.0472

Gnomad4 SAS exome AF: 0.0491

Gnomad4 FIN exome AF: 0.00158

Gnomad4 NFE exome AF: 0.00168

Gnomad4 OTH exome AF: 0.00835

GnomAD4 genome AF: 0.00597 AC: 909 AN: 152332 Hom.: 18 Cov.: 32 AF XY: 0.00726 AC XY: 541 AN XY: 74488

Gnomad4 AFR AF: 0.000698

Gnomad4 AMR AF: 0.00209

Gnomad4 ASJ AF: 0.00432

Gnomad4 EAS AF: 0.0690

Gnomad4 SAS AF: 0.0550

Gnomad4 FIN AF: 0.000942

Gnomad4 NFE AF: 0.00263

Gnomad4 OTH AF: 0.00615

Alfa AF: 0.00344 Hom.: 0

Bravo AF: 0.00550

Asia WGS AF: 0.0540 AC: 187 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	7.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs75560005; hg19: chr6-29603782;