14-77260014-A-G

Position:

• chr14-77260014-A-G

Variant summary

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

The XR_007064276.1(LOC124903351):​n.196A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 152,114 control chromosomes in the GnomAD database, including 51,667 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 0.82 (51667 hom., cov: 31)
• Consequence: LOC124903351 XR_007064276.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114

Genes affected

LOC124903351 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903351	XR_007064276.1	n.196A>G		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125074 AN: 151996 Hom.: 51617 Cov.: 31

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.850

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.823 AC: 125180 AN: 152114 Hom.: 51667 Cov.: 31 AF XY: 0.825 AC XY: 61358 AN XY: 74364

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.855

Gnomad4 EAS AF: 0.955

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.836

Alfa AF: 0.824 Hom.: 6427

Bravo AF: 0.820

Asia WGS AF: 0.888 AC: 3091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.2
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs369202; hg19: chr14-77726357;