rs600469

chr6-137640535-C-T

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 0.536 in 151,942 control chromosomes in the GnomAD database, including 21,803 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 0.54 (21803 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 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: 0.535 AC: 81294 AN: 151824 Hom.: 21770 Cov.: 31

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.536 AC: 81375 AN: 151942 Hom.: 21803 Cov.: 31 AF XY: 0.532 AC XY: 39503 AN XY: 74278

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.521

Alfa AF: 0.523 Hom.: 10556

Bravo AF: 0.546

Asia WGS AF: 0.486 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.37
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs600469; hg19: chr6-137961672;