rs9942977

Variant names:

• chr9-106620080-G-A
• rs9942977
• ENST00000411451.3:n.187-44673G>A

Variant summary

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

The ENST00000411451.3(LINC01505):​n.187-44673G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,194 control chromosomes in the GnomAD database, including 2,448 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 0.15 (2448 hom., cov: 33)
• Consequence: LINC01505 ENST00000411451.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01505	NR_104145.1	n.259+3764G>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01505	ENST00000411451.3	n.187-44673G>A		intron_variant	Intron 2 of 5	3
LINC01505	ENST00000444985.7	n.263+3764G>A		intron_variant	Intron 1 of 6	2
LINC01505	ENST00000637185.1	n.760-18079G>A		intron_variant	Intron 3 of 7	5

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22899 AN: 152076 Hom.: 2439 Cov.: 33

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.0736

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0268

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.0575

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0964

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.151 AC: 22941 AN: 152194 Hom.: 2448 Cov.: 33 AF XY: 0.151 AC XY: 11259 AN XY: 74424

African (AFR) AF: 0.287 AC: 11930 AN: 41508

American (AMR) AF: 0.0734 AC: 1122 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 503 AN: 3472

East Asian (EAS) AF: 0.0267 AC: 138 AN: 5176

South Asian (SAS) AF: 0.333 AC: 1602 AN: 4818

European-Finnish (FIN) AF: 0.0575 AC: 610 AN: 10608

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0964 AC: 6555 AN: 68000

Other (OTH) AF: 0.135 AC: 284 AN: 2110

Alfa AF: 0.116 Hom.: 1106

Bravo AF: 0.151

Asia WGS AF: 0.192 AC: 668 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.7
DANN	Benign	0.77
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs9942977; hg19: chr9-109382361;