6-14142258-G-C

Position:

• chr6-14142258-G-C

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 0.62 in 150,588 control chromosomes in the GnomAD database, including 29,538 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 0.62 (29538 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.619 AC: 93208 AN: 150468 Hom.: 29492 Cov.: 25

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.620 AC: 93323 AN: 150588 Hom.: 29538 Cov.: 25 AF XY: 0.617 AC XY: 45344 AN XY: 73482

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.620

Alfa AF: 0.501 Hom.: 1369

Bravo AF: 0.623

Asia WGS AF: 0.358 AC: 1248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs853369; hg19: chr6-14142489;