rs1113000

chr14-62666686-G-A

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 0.25 in 151,952 control chromosomes in the GnomAD database, including 4,857 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 0.25 (4857 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.283 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: 0.250 AC: 38032 AN: 151834 Hom.: 4866 Cov.: 31

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.250 AC: 38035 AN: 151952 Hom.: 4857 Cov.: 31 AF XY: 0.250 AC XY: 18546 AN XY: 74250

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.263

Alfa AF: 0.253 Hom.: 1045

Bravo AF: 0.258

Asia WGS AF: 0.265 AC: 921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.26
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1113000; hg19: chr14-63133404;