6-160698207-C-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 0.263 in 152,136 control chromosomes in the GnomAD database, including 6,328 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 0.26 (6327 hom., cov: 31)
  • Exomes 𝑓: 0.22 (1 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 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: 0.263 AC: 40044 AN: 151986 Hom.: 6329 Cov.: 31

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.275

GnomAD4 exome AF: 0.219 AC: 7 AN: 32 Hom.: 1 AF XY: 0.192 AC XY: 5 AN XY: 26

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.233

GnomAD4 genome AF: 0.263 AC: 40049 AN: 152104 Hom.: 6327 Cov.: 31 AF XY: 0.270 AC XY: 20103 AN XY: 74338

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.272

Alfa AF: 0.166 Hom.: 373

Bravo AF: 0.270

Asia WGS AF: 0.447 AC: 1553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.5
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: rs783144; hg19: chr6-161119239; COSMIC: COSV51981736;