rs6573908

Positions:

• chr14-69772247-A-C
• chr14-69772247-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 0.367 in 152,076 control chromosomes in the GnomAD database, including 12,208 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 0.37 (12208 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 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: 0.366 AC: 55636 AN: 151960 Hom.: 12156 Cov.: 33

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.367 AC: 55755 AN: 152076 Hom.: 12208 Cov.: 33 AF XY: 0.363 AC XY: 26978 AN XY: 74344

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.357

Alfa AF: 0.275 Hom.: 8245

Bravo AF: 0.384

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.085
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6573908; hg19: chr14-70238964;