rs988131

Positions:

• chr14-106776833-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 0.199 in 152,092 control chromosomes in the GnomAD database, including 3,489 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 0.20 (3489 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 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: 0.199 AC: 30174 AN: 151974 Hom.: 3481 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.199 AC: 30211 AN: 152092 Hom.: 3489 Cov.: 33 AF XY: 0.198 AC XY: 14692 AN XY: 74354

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.218

Alfa AF: 0.163 Hom.: 386

Bravo AF: 0.207

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.9
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs988131; hg19: chr14-107185072;