6-49403271-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 0.645 in 151,774 control chromosomes in the GnomAD database, including 31,754 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 0.65 (31754 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 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: 0.645 AC: 97834 AN: 151654 Hom.: 31727 Cov.: 30

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.645 AC: 97910 AN: 151774 Hom.: 31754 Cov.: 30 AF XY: 0.648 AC XY: 48072 AN XY: 74148

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.667

Alfa AF: 0.642 Hom.: 15904

Bravo AF: 0.657

Asia WGS AF: 0.658 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.2
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2501976; hg19: chr6-49370984;