rs1106494

Variant names:

• chr14-62665263-G-A
• rs1106494

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.151 AC: 6249 AN: 41498

American (AMR) AF: 0.387 AC: 5919 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1139 AN: 3470

East Asian (EAS) AF: 0.361 AC: 1860 AN: 5158

South Asian (SAS) AF: 0.428 AC: 2064 AN: 4826

European-Finnish (FIN) AF: 0.422 AC: 4456 AN: 10570

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29108 AN: 67984

Other (OTH) AF: 0.349 AC: 737 AN: 2110

Alfa AF: 0.365 Hom.: 2986

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
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs1106494; hg19: chr14-63131981;