XR_007067915.1:n.4634C>T

Variant names:

• chr21-46451672-G-A
• rs1010111
• XR_007067915.1:n.4634C>T

Variant summary

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

The XR_007067915.1(LOC124905046):​n.4634C>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 0.726 in 152,206 control chromosomes in the GnomAD database, including 40,175 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 0.73 (40175 hom., cov: 34)
• Consequence: LOC124905046 XR_007067915.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.910
• Publications: 1 publications found

Genes affected

LOC124905046 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124905046	XR_007067915.1	n.4634C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289421	ENST00000689761.2	n.388-3073C>T		intron_variant	Intron 1 of 1
ENSG00000289421	ENST00000796412.1	n.553-3073C>T		intron_variant	Intron 1 of 1
ENSG00000289421	ENST00000796413.1	n.632-3073C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.726 AC: 110350 AN: 152088 Hom.: 40143 Cov.: 34

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.726 AC: 110443 AN: 152206 Hom.: 40175 Cov.: 34 AF XY: 0.720 AC XY: 53602 AN XY: 74396

African (AFR) AF: 0.722 AC: 29971 AN: 41524

American (AMR) AF: 0.689 AC: 10544 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2555 AN: 3470

East Asian (EAS) AF: 0.796 AC: 4121 AN: 5178

South Asian (SAS) AF: 0.748 AC: 3608 AN: 4826

European-Finnish (FIN) AF: 0.655 AC: 6932 AN: 10576

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50300 AN: 68014

Other (OTH) AF: 0.737 AC: 1558 AN: 2114

Alfa AF: 0.716 Hom.: 5048

Bravo AF: 0.728

Asia WGS AF: 0.760 AC: 2647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.14
DANN	Benign	0.28
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs1010111; hg19: chr21-47871585;