rs204426

Variant names:

• chr6-153942850-T-C
• rs204426

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;