XR_007064176.1:n.9020G>T

Variant names:

• chr14-53602063-C-A
• rs210327
• XR_007064176.1:n.9020G>T

Variant summary

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

The XR_007064176.1(LOC124903316):​n.9020G>T 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 0.618 in 152,050 control chromosomes in the GnomAD database, including 30,045 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 0.62 (30045 hom., cov: 32)
• Consequence: LOC124903316 XR_007064176.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

Genes affected

LOC124903316 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903316	XR_007064176.1	n.9020G>T		non_coding_transcript_exon_variant	Exon 2 of 2
LOC105370504	XR_001750974.1	n.3896-85136C>A		intron_variant	Intron 2 of 2
LOC105370504	XR_001750975.3	n.29701-85136C>A		intron_variant	Intron 2 of 2
LOC105370504	XR_943876.3	n.29701-85136C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225680	ENST00000436530.1	n.375-1880G>T		intron_variant	Intron 1 of 1	3
ENSG00000237356	ENST00000456100.6	n.326-85136C>A		intron_variant	Intron 3 of 3	4
ENSG00000237356	ENST00000648066.1	n.335-85136C>A		intron_variant	Intron 4 of 9

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93873 AN: 151932 Hom.: 29989 Cov.: 32

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.618 AC: 93991 AN: 152050 Hom.: 30045 Cov.: 32 AF XY: 0.610 AC XY: 45361 AN XY: 74310

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.614

Alfa AF: 0.579 Hom.: 36261

Bravo AF: 0.621

Asia WGS AF: 0.512 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.26
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs210327; hg19: chr14-54068781;