rs1106494

Variant names:

• chr14-62665263-G-A
• rs1106494

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 0.342 in 152,104 control chromosomes in the GnomAD database, including 10,066 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 0.34 (10066 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105

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 (NFE) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.342 AC: 52002 AN: 151984 Hom.: 10069 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.342 AC: 52012 AN: 152104 Hom.: 10066 Cov.: 33 AF XY: 0.347 AC XY: 25763 AN XY: 74334

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.349

Alfa AF: 0.370 Hom.: 2976

Bravo AF: 0.327

Asia WGS AF: 0.395 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1106494; hg19: chr14-63131981;