6-43767412-G-T

Variant names:

• chr6-43767412-G-T
• rs833060

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 0.251 in 152,196 control chromosomes in the GnomAD database, including 4,922 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 0.25 (4922 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 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: 0.251 AC: 38125 AN: 152078 Hom.: 4917 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.251 AC: 38133 AN: 152196 Hom.: 4922 Cov.: 33 AF XY: 0.249 AC XY: 18552 AN XY: 74396

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.274

Alfa AF: 0.235 Hom.: 528

Bravo AF: 0.261

Asia WGS AF: 0.274 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs833060; hg19: chr6-43735149;