ENST00000637185.1:n.559+170919C>A

Variant names:

• chr9-106164787-C-A
• rs7028916
• ENST00000637185.1:n.559+170919C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000637185.1(LINC01505):​n.559+170919C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,810 control chromosomes in the GnomAD database, including 7,289 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 0.31 (7289 hom., cov: 32)
• Consequence: LINC01505 ENST00000637185.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 9 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987108	XR_001746870.2	n.2032+188656C>A		intron_variant	Intron 3 of 5
LOC107987108	XR_007061713.1	n.2032+188656C>A		intron_variant	Intron 3 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01505	ENST00000637185.1	n.559+170919C>A		intron_variant	Intron 1 of 7	5

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46594 AN: 151692 Hom.: 7265 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.260

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.307 AC: 46661 AN: 151810 Hom.: 7289 Cov.: 32 AF XY: 0.309 AC XY: 22921 AN XY: 74186

African (AFR) AF: 0.346 AC: 14318 AN: 41424

American (AMR) AF: 0.289 AC: 4396 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1003 AN: 3468

East Asian (EAS) AF: 0.433 AC: 2231 AN: 5148

South Asian (SAS) AF: 0.190 AC: 910 AN: 4796

European-Finnish (FIN) AF: 0.319 AC: 3354 AN: 10500

Middle Eastern (MID) AF: 0.272 AC: 79 AN: 290

European-Non Finnish (NFE) AF: 0.287 AC: 19511 AN: 67950

Other (OTH) AF: 0.297 AC: 625 AN: 2102

Alfa AF: 0.293 Hom.: 27604

Bravo AF: 0.308

Asia WGS AF: 0.276 AC: 964 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.5
DANN	Benign	0.58
PhyloP100		0.036

Splicing

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

Other links and lift over

dbSNP: rs7028916; hg19: chr9-108927068;