rs11869614

Variant names:

• chr17-16451729-C-T
• rs11869614
• NM_001113567.3:c.376-3769G>A

Variant summary

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

The NM_001113567.3(LRRC75A):​c.376-3769G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 151,600 control chromosomes in the GnomAD database, including 4,154 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 0.23 (4154 hom., cov: 28)
• Consequence: LRRC75A NM_001113567.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.06
• Publications: 23 publications found

Genes affected

LRRC75A (HGNC:32403): (leucine rich repeat containing 75A) Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

SNHG29 (HGNC:28619): (small nucleolar RNA host gene 29)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001113567.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC75A	NM_001113567.3	MANE Select	c.376-3769G>A		intron	N/A	NP_001107039.1	Q8NAA5-1
	LRRC75A	NM_207387.4		c.376-7598G>A		intron	N/A	NP_997270.2	Q8NAA5-2
	SNHG29	NR_027171.1		n.554+10599C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC75A	ENST00000470794.2	TSL:1 MANE Select	c.376-3769G>A		intron	N/A	ENSP00000419502.1	Q8NAA5-1
	SNHG29	ENST00000581361.5	TSL:1	n.182-9164C>T		intron	N/A
	LRRC75A	ENST00000934493.1		c.376-3769G>A		intron	N/A	ENSP00000604552.1

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34368 AN: 151484 Hom.: 4158 Cov.: 28

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0319

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.227 AC: 34369 AN: 151600 Hom.: 4154 Cov.: 28 AF XY: 0.222 AC XY: 16457 AN XY: 74074

African (AFR) AF: 0.193 AC: 7995 AN: 41360

American (AMR) AF: 0.187 AC: 2847 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 723 AN: 3466

East Asian (EAS) AF: 0.0318 AC: 163 AN: 5128

South Asian (SAS) AF: 0.181 AC: 864 AN: 4786

European-Finnish (FIN) AF: 0.189 AC: 1974 AN: 10442

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 18996 AN: 67872

Other (OTH) AF: 0.243 AC: 513 AN: 2110

Alfa AF: 0.263 Hom.: 19819

Bravo AF: 0.224

Asia WGS AF: 0.125 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.0
DANN	Benign	0.63
PhyloP100		-3.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11869614; hg19: chr17-16355043;