6-39249743-C-T

Variant names:

• chr6-39249743-C-T
• rs1616076

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 0.46 in 151,948 control chromosomes in the GnomAD database, including 19,748 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 0.46 (19748 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.38

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 (AFR) allele frequency at 95% confidence interval = 0.764 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: 0.460 AC: 69866 AN: 151830 Hom.: 19709 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.460 AC: 69971 AN: 151948 Hom.: 19748 Cov.: 32 AF XY: 0.466 AC XY: 34630 AN XY: 74264

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.475

Alfa AF: 0.174 Hom.: 313

Bravo AF: 0.485

Asia WGS AF: 0.556 AC: 1934 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	0.023
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: rs1616076; hg19: chr6-39217519;