rs11869614

Positions:

• chr17-16451729-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC75A	NM_001113567.3	c.376-3769G>A		intron_variant		ENST00000470794.2
SNHG29	NR_027171.1	n.554+10599C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC75A	ENST00000470794.2	c.376-3769G>A		intron_variant		1	NM_001113567.3	P1
SNHG29	ENST00000702366.1	n.238+10599C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.0318

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.243

Alfa AF: 0.269 Hom.: 9789

Bravo AF: 0.224

Asia WGS AF: 0.125 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.0
DANN	Benign	0.63

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

Publications

LitVar

Other links and lift over

dbSNP: rs11869614; hg19: chr17-16355043;