rs7772131

Variant names:

• chr6-30827394-A-C
• rs7772131
• ENST00000399196.1:n.145+3121T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000399196.1(LINC00243):​n.145+3121T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0193 in 152,096 control chromosomes in the GnomAD database, including 48 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 0.019 (48 hom., cov: 32)
• Consequence: LINC00243 ENST00000399196.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

Genes affected

LINC00243 (HGNC:30956): (long intergenic non-protein coding RNA 243)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0193 (2930/152096) while in subpopulation AMR AF= 0.033 (504/15268). AF 95% confidence interval is 0.0306. There are 48 homozygotes in gnomad4. There are 1348 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 48 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00243	NR_130726.1	n.145+3121T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00243	ENST00000399196.1	n.145+3121T>G		intron_variant	Intron 1 of 1	2
LINC00243	ENST00000419357.6	n.145+3121T>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.0193 AC: 2927 AN: 151978 Hom.: 48 Cov.: 32

Gnomad AFR AF: 0.0281

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0330

Gnomad ASJ AF: 0.0744

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.000472

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0193 AC: 2930 AN: 152096 Hom.: 48 Cov.: 32 AF XY: 0.0181 AC XY: 1348 AN XY: 74364

Gnomad4 AFR AF: 0.0281

Gnomad4 AMR AF: 0.0330

Gnomad4 ASJ AF: 0.0744

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00187

Gnomad4 FIN AF: 0.000472

Gnomad4 NFE AF: 0.0137

Gnomad4 OTH AF: 0.0246

Alfa AF: 0.0169 Hom.: 31

Bravo AF: 0.0229

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7772131; hg19: chr6-30795171;