6-14141866-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.263 in 152,150 control chromosomes in the GnomAD database, including 6,121 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 (6121 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 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: 39964 AN: 152032 Hom.: 6092 Cov.: 31

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.263 AC: 40064 AN: 152150 Hom.: 6121 Cov.: 31 AF XY: 0.261 AC XY: 19442 AN XY: 74382

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.276

Alfa AF: 0.187 Hom.: 821

Bravo AF: 0.274

Asia WGS AF: 0.148 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
Cadd	Benign	17
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs750749; hg19: chr6-14142097;