rs6827408

chr4-60312113-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 0.697 in 151,914 control chromosomes in the GnomAD database, including 38,938 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 0.70 (38938 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.951

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 (NFE) allele frequency at 95% confidence interval = 0.82 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: 0.697 AC: 105806 AN: 151794 Hom.: 38941 Cov.: 31

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.847

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.697 AC: 105824 AN: 151914 Hom.: 38938 Cov.: 31 AF XY: 0.693 AC XY: 51500 AN XY: 74264

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.716

Alfa AF: 0.804 Hom.: 43527

Bravo AF: 0.687

Asia WGS AF: 0.514 AC: 1789 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	0.087
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6827408; hg19: chr4-61177831;