rs17354216

chr6-14139472-T-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 0.064 in 152,302 control chromosomes in the GnomAD database, including 351 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 0.064 (351 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0721 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: 0.0638 AC: 9711 AN: 152184 Hom.: 346 Cov.: 32

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.0236

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0340

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0585

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0640 AC: 9740 AN: 152302 Hom.: 351 Cov.: 32 AF XY: 0.0651 AC XY: 4849 AN XY: 74466

Gnomad4 AFR AF: 0.0742

Gnomad4 AMR AF: 0.0731

Gnomad4 ASJ AF: 0.0236

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0336

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.0585

Gnomad4 OTH AF: 0.0563

Alfa AF: 0.0602 Hom.: 299

Bravo AF: 0.0641

Asia WGS AF: 0.0270 AC: 92 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.28
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17354216; hg19: chr6-14139703;