rs7536479

Variant names:

• chr1-99600012-A-G
• rs7536479
• ENST00000635551.1:n.163+300T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-99600012-A-G
• chr1-99600012-A-T

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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01708	ENST00000635551.1	n.163+300T>C		intron_variant	Intron 2 of 4	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;