chr1-99600012-A-G

Position:

• chr1-99600012-A-G

Variant summary

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

The ENST00000635551.1(LINC01708):​n.163+300T>C 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 0.759 in 152,066 control chromosomes in the GnomAD database, including 44,237 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 0.76 (44237 hom., cov: 31)
• Consequence: LINC01708 ENST00000635551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364

Genes affected

LINC01708 (HGNC:52496): (long intergenic non-protein coding RNA 1708)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01708	ENST00000635551.1	n.163+300T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115298 AN: 151948 Hom.: 44181 Cov.: 31

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.759 AC: 115419 AN: 152066 Hom.: 44237 Cov.: 31 AF XY: 0.756 AC XY: 56161 AN XY: 74314

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.737

Alfa AF: 0.739 Hom.: 26931

Bravo AF: 0.748

Asia WGS AF: 0.650 AC: 2261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.65
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7536479; hg19: chr1-100065568;