rs6469653

Variant names:

• chr8-116619725-G-A
• rs6469653

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 0.454 in 151,284 control chromosomes in the GnomAD database, including 18,048 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 0.45 (18048 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.597 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: 0.454 AC: 68602 AN: 151186 Hom.: 18055 Cov.: 30

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.454 AC: 68618 AN: 151284 Hom.: 18048 Cov.: 30 AF XY: 0.452 AC XY: 33383 AN XY: 73814

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.497

Alfa AF: 0.572 Hom.: 50664

Bravo AF: 0.432

Asia WGS AF: 0.345 AC: 1200 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	3.5
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6469653; hg19: chr8-117631964;