chr1-83849071-G-A

Position:

• chr1-83849071-G-A

Variant summary

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

The NR_119374.1(LOC101927560):​n.255+836C>T variant causes a intron, non coding transcript 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: LOC101927560 NR_119374.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

Genes affected

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

LOC101927560 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC101927560	NR_119374.1	n.255+836C>T		intron_variant, non_coding_transcript_variant
LINC01725	NR_119375.1	n.178+11748C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01725	ENST00000417975.1	n.178+11748C>T		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.886

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.907

Gnomad4 SAS AF: 0.881

Gnomad4 FIN AF: 0.819

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.832

Alfa AF: 0.845 Hom.: 25718

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10747407; hg19: chr1-84314754;