rs7772131

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 48 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000399196.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00243	NR_130726.1		n.145+3121T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00243	ENST00000399196.1	TSL:2	n.145+3121T>G		intron	N/A
	LINC00243	ENST00000419357.7	TSL:3	n.145+3121T>G		intron	N/A
	LINC00243	ENST00000719489.1		n.127+3121T>G		intron	N/A

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

African (AFR) AF: 0.0281 AC: 1165 AN: 41480

American (AMR) AF: 0.0330 AC: 504 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0744 AC: 258 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.00187 AC: 9 AN: 4824

European-Finnish (FIN) AF: 0.000472 AC: 5 AN: 10590

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0137 AC: 929 AN: 67968

Other (OTH) AF: 0.0246 AC: 52 AN: 2110

Alfa AF: 0.0179 Hom.: 113

Bravo AF: 0.0229

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.5
DANN	Benign	0.72
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs7772131; hg19: chr6-30795171;