rs10747407

Variant names:

• chr1-83849071-G-A
• rs10747407
• ENST00000417975.1:n.178+11748C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-83849071-G-A
• chr1-83849071-G-C
• chr1-83849071-G-T

Variant summary

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

The ENST00000417975.1(LINC01725):​n.178+11748C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 152,188 control chromosomes in the GnomAD database, including 55,668 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 0.85 (55668 hom., cov: 32)
• Consequence: LINC01725 ENST00000417975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 2 publications found

Genes affected

LINC01725 (HGNC:52513): (long intergenic non-protein coding RNA 1725)

LOC101927560 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927560	NR_119374.1	n.255+836C>T		intron_variant	Intron 2 of 2
LINC01725	NR_119375.1	n.178+11748C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01725	ENST00000417975.1	n.178+11748C>T		intron_variant	Intron 1 of 2	1
LINC01725	ENST00000413975.7	n.213+11748C>T		intron_variant	Intron 1 of 1	2
LINC01725	ENST00000417565.6	n.316+836C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129943 AN: 152070 Hom.: 55627 Cov.: 32

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.854 AC: 130036 AN: 152188 Hom.: 55668 Cov.: 32 AF XY: 0.855 AC XY: 63637 AN XY: 74394

African (AFR) AF: 0.883 AC: 36650 AN: 41524

American (AMR) AF: 0.886 AC: 13548 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2753 AN: 3472

East Asian (EAS) AF: 0.907 AC: 4695 AN: 5178

South Asian (SAS) AF: 0.881 AC: 4247 AN: 4822

European-Finnish (FIN) AF: 0.819 AC: 8672 AN: 10592

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56845 AN: 67990

Other (OTH) AF: 0.832 AC: 1758 AN: 2112

Alfa AF: 0.845 Hom.: 28771

Bravo AF: 0.859

Asia WGS AF: 0.844 AC: 2932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.79
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs10747407; hg19: chr1-84314754;