6-103335483-T-C

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 0.865 in 152,096 control chromosomes in the GnomAD database, including 56,973 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 0.87 (56973 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 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: 0.865 AC: 131515 AN: 151978 Hom.: 56945 Cov.: 30

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.885

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.865 AC: 131595 AN: 152096 Hom.: 56973 Cov.: 30 AF XY: 0.866 AC XY: 64390 AN XY: 74330

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.857

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.897

Gnomad4 NFE AF: 0.866

Gnomad4 OTH AF: 0.868

Alfa AF: 0.863 Hom.: 44029

Bravo AF: 0.859

Asia WGS AF: 0.886 AC: 3079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.21
Dann	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2399927; hg19: chr6-103783358;