rs4424056

chr6-91135689-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.768 in 152,096 control chromosomes in the GnomAD database, including 45,299 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 0.77 (45299 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.08

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 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: 0.768 AC: 116781 AN: 151978 Hom.: 45262 Cov.: 33

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.768 AC: 116866 AN: 152096 Hom.: 45299 Cov.: 33 AF XY: 0.772 AC XY: 57399 AN XY: 74350

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.847

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.754

Alfa AF: 0.787 Hom.: 77466

Bravo AF: 0.764

Asia WGS AF: 0.893 AC: 3101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
Cadd	Benign	23
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4424056; hg19: chr6-91845407;