6-108010090-A-T

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 0.397 in 152,066 control chromosomes in the GnomAD database, including 17,409 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 0.40 (17409 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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: 0.397 AC: 60313 AN: 151946 Hom.: 17349 Cov.: 32

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.397 AC: 60438 AN: 152066 Hom.: 17409 Cov.: 32 AF XY: 0.396 AC XY: 29460 AN XY: 74338

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.342

Alfa AF: 0.149 Hom.: 275

Bravo AF: 0.423

Asia WGS AF: 0.366 AC: 1273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	5.4
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4946888; hg19: chr6-108331294; COSMIC: COSV68860252;