6-18519435-T-G

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 0.378 in 152,032 control chromosomes in the GnomAD database, including 12,046 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 0.38 (12046 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549

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 (AFR) allele frequency at 95% confidence interval = 0.563 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: 0.377 AC: 57346 AN: 151914 Hom.: 12021 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.0949

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.378 AC: 57421 AN: 152032 Hom.: 12046 Cov.: 32 AF XY: 0.372 AC XY: 27615 AN XY: 74324

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.0945

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.353

Alfa AF: 0.209 Hom.: 420

Bravo AF: 0.398

Asia WGS AF: 0.179 AC: 620 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.7
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4716278; hg19: chr6-18519666;