14-77260014-A-G

Variant names:

• chr14-77260014-A-G
• rs369202
• XR_007064276.1:n.196A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

LOC124903351 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124903351	XR_007064276.1	n.196A>G		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.856 AC: 35512 AN: 41488

American (AMR) AF: 0.765 AC: 11689 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2966 AN: 3468

East Asian (EAS) AF: 0.955 AC: 4935 AN: 5170

South Asian (SAS) AF: 0.809 AC: 3897 AN: 4816

European-Finnish (FIN) AF: 0.847 AC: 8973 AN: 10600

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.801 AC: 54448 AN: 67978

Other (OTH) AF: 0.836 AC: 1767 AN: 2114

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
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs369202; hg19: chr14-77726357;