rs204426

chr6-153942850-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 0.557 in 151,896 control chromosomes in the GnomAD database, including 23,904 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 0.56 (23904 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.62 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: 0.557 AC: 84544 AN: 151778 Hom.: 23883 Cov.: 31

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.557 AC: 84598 AN: 151896 Hom.: 23904 Cov.: 31 AF XY: 0.554 AC XY: 41117 AN XY: 74214

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.558

Alfa AF: 0.591 Hom.: 12849

Bravo AF: 0.547

Asia WGS AF: 0.421 AC: 1465 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.082
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs204426; hg19: chr6-154263985;