rs6919479

Variant names:

• chr6-44485358-T-C
• rs6919479

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 0.582 in 151,818 control chromosomes in the GnomAD database, including 26,114 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 0.58 (26114 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.655 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: 0.582 AC: 88316 AN: 151700 Hom.: 26104 Cov.: 31

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.582 AC: 88361 AN: 151818 Hom.: 26114 Cov.: 31 AF XY: 0.585 AC XY: 43429 AN XY: 74184

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.602

Alfa AF: 0.606 Hom.: 3405

Bravo AF: 0.571

Asia WGS AF: 0.644 AC: 2238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6919479; hg19: chr6-44453095;