rs269434

chr6-88014148-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 0.882 in 152,194 control chromosomes in the GnomAD database, including 59,360 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 0.88 (59360 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.999

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.887 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: 0.882 AC: 134197 AN: 152076 Hom.: 59328 Cov.: 30

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.882 AC: 134284 AN: 152194 Hom.: 59360 Cov.: 30 AF XY: 0.881 AC XY: 65598 AN XY: 74426

Gnomad4 AFR AF: 0.882

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.870

Gnomad4 EAS AF: 0.791

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.945

Gnomad4 NFE AF: 0.893

Gnomad4 OTH AF: 0.887

Alfa AF: 0.887 Hom.: 10492

Bravo AF: 0.876

Asia WGS AF: 0.799 AC: 2779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	14
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs269434; hg19: chr6-88723866;