chr9-106238610-T-C

Variant names:

• chr9-106238610-T-C
• rs7030412
• ENST00000637185.1:n.559+244742T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000637185.1(LINC01505):​n.559+244742T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0145 in 152,270 control chromosomes in the GnomAD database, including 26 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 0.015 (26 hom., cov: 32)
• Consequence: LINC01505 ENST00000637185.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 0 publications found

Genes affected

LINC01505 (HGNC:51186): (long intergenic non-protein coding RNA 1505)

LOC107987108 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0145 (2209/152270) while in subpopulation AFR AF = 0.0284 (1181/41574). AF 95% confidence interval is 0.0271. There are 26 homozygotes in GnomAd4. There are 1034 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 26 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637185.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01505	ENST00000637185.1	TSL:5	n.559+244742T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0144 AC: 2191 AN: 152152 Hom.: 22 Cov.: 32

Gnomad AFR AF: 0.0280

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00819

Gnomad ASJ AF: 0.00779

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00269

Gnomad FIN AF: 0.00631

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0112

Gnomad OTH AF: 0.0162

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

GnomAD4 genome AF: 0.0145 AC: 2209 AN: 152270 Hom.: 26 Cov.: 32 AF XY: 0.0139 AC XY: 1034 AN XY: 74442

African (AFR) AF: 0.0284 AC: 1181 AN: 41574

American (AMR) AF: 0.00812 AC: 124 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00779 AC: 27 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.00270 AC: 13 AN: 4822

European-Finnish (FIN) AF: 0.00631 AC: 67 AN: 10610

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0112 AC: 759 AN: 68020

Other (OTH) AF: 0.0161 AC: 34 AN: 2116

Alfa AF: 0.0129 Hom.: 19

Bravo AF: 0.0158

Asia WGS AF: 0.00636 AC: 22 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.3
DANN	Benign	0.77
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs7030412; hg19: chr9-109000891;