XR_007059467.1:n.14458A>C

Variant names:

• chr6-14471294-A-C
• rs979037
• XR_007059467.1:n.14458A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007059467.1(LOC101928331):​n.14458A>C 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 0.52 in 152,092 control chromosomes in the GnomAD database, including 21,696 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 0.52 (21696 hom., cov: 32)
• Consequence: LOC101928331 XR_007059467.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72
• Publications: 2 publications found

Genes affected

LOC101928331 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928331	XR_007059467.1	n.14458A>C		non_coding_transcript_exon_variant	Exon 2 of 2
LOC101928331	XR_001743994.3	n.296-26763A>C		intron_variant	Intron 1 of 2
LOC101928331	XR_001743997.3	n.139-26763A>C		intron_variant	Intron 1 of 3
LOC101928331	XR_001743999.3	n.139-26763A>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286277	ENST00000666857.2	n.520-26763A>C		intron_variant	Intron 1 of 2
ENSG00000234261	ENST00000729738.1	n.374-10773T>G		intron_variant	Intron 4 of 7
ENSG00000234261	ENST00000729739.1	n.310-9344T>G		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78939 AN: 151972 Hom.: 21652 Cov.: 32

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.520 AC: 79050 AN: 152092 Hom.: 21696 Cov.: 32 AF XY: 0.521 AC XY: 38716 AN XY: 74340

African (AFR) AF: 0.660 AC: 27392 AN: 41486

American (AMR) AF: 0.554 AC: 8463 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1343 AN: 3472

East Asian (EAS) AF: 0.728 AC: 3766 AN: 5176

South Asian (SAS) AF: 0.686 AC: 3309 AN: 4826

European-Finnish (FIN) AF: 0.369 AC: 3898 AN: 10562

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29176 AN: 67978

Other (OTH) AF: 0.494 AC: 1039 AN: 2102

Alfa AF: 0.396 Hom.: 1706

Bravo AF: 0.537

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	19
DANN	Benign	0.89
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs979037; hg19: chr6-14471525;