chr6-52144499-C-T

Position:

• chr6-52144499-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.00602 in 480,818 control chromosomes in the GnomAD database, including 11 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 0.0057 (2 hom., cov: 32)
  • Exomes 𝑓: 0.0062 (9 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00618 (2029/328476) while in subpopulation MID AF= 0.022 (56/2542). AF 95% confidence interval is 0.0174. There are 9 homozygotes in gnomad4_exome. There are 1073 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 2 gene

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: 0.00568 AC: 865 AN: 152224 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.00176

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.00870

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.00151

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00858

Gnomad OTH AF: 0.0105

GnomAD4 exome AF: 0.00618 AC: 2029 AN: 328476 Hom.: 9 AF XY: 0.00586 AC XY: 1073 AN XY: 183158

Gnomad4 AFR exome AF: 0.00197

Gnomad4 AMR exome AF: 0.00528

Gnomad4 ASJ exome AF: 0.00372

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00254

Gnomad4 FIN exome AF: 0.00124

Gnomad4 NFE exome AF: 0.00922

Gnomad4 OTH exome AF: 0.00784

GnomAD4 genome AF: 0.00568 AC: 865 AN: 152342 Hom.: 2 Cov.: 32 AF XY: 0.00546 AC XY: 407 AN XY: 74502

Gnomad4 AFR AF: 0.00176

Gnomad4 AMR AF: 0.00869

Gnomad4 ASJ AF: 0.00548

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00166

Gnomad4 FIN AF: 0.00151

Gnomad4 NFE AF: 0.00858

Gnomad4 OTH AF: 0.0104

Alfa AF: 0.00706 Hom.: 0

Bravo AF: 0.00629

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	-0.85
CADD	Benign	6.8
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17578796; hg19: chr6-52009297;