chr14-40598733-A-G

Position:

• chr14-40598733-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_943790.3(LOC105370466):​n.829+13630T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,518 control chromosomes in the GnomAD database, including 18,287 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 0.48 (18287 hom., cov: 31)
• Consequence: LOC105370466 XR_943790.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

Genes affected

LOC105370466 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370466	XR_943790.3	n.829+13630T>C		intron_variant, non_coding_transcript_variant
LOC105370466	XR_943792.3	n.840-5571T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72064 AN: 151400 Hom.: 18265 Cov.: 31

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.476 AC: 72142 AN: 151518 Hom.: 18287 Cov.: 31 AF XY: 0.480 AC XY: 35507 AN XY: 74014

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.454

Alfa AF: 0.423 Hom.: 1821

Bravo AF: 0.490

Asia WGS AF: 0.532 AC: 1822 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9323032; hg19: chr14-41067938;