rs10484042

Positions:

• chr14-94397364-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 0.0472 in 152,170 control chromosomes in the GnomAD database, including 388 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 0.047 (388 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.94397364G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289541	ENST00000693506.1	n.124+6470G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0472 AC: 7171 AN: 152052 Hom.: 385 Cov.: 33

Gnomad AFR AF: 0.0116

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0279

Gnomad EAS AF: 0.00520

Gnomad SAS AF: 0.0915

Gnomad FIN AF: 0.0279

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.0426

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

GnomAD4 genome AF: 0.0472 AC: 7184 AN: 152170 Hom.: 388 Cov.: 33 AF XY: 0.0510 AC XY: 3793 AN XY: 74392

Gnomad4 AFR AF: 0.0116

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.0279

Gnomad4 EAS AF: 0.00502

Gnomad4 SAS AF: 0.0918

Gnomad4 FIN AF: 0.0279

Gnomad4 NFE AF: 0.0460

Gnomad4 OTH AF: 0.0422

Alfa AF: 0.0493 Hom.: 76

Bravo AF: 0.0539

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484042; hg19: chr14-94863701;