rs8082268

Variant names:

• chr17-16453005-T-C
• rs8082268
• NM_001113567.3:c.376-5045A>G

Variant summary

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

The NM_001113567.3(LRRC75A):​c.376-5045A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 151,774 control chromosomes in the GnomAD database, including 28,693 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 0.61 (28693 hom., cov: 30)
• Consequence: LRRC75A NM_001113567.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC75A	NM_001113567.3	c.376-5045A>G		intron_variant	Intron 2 of 3	ENST00000470794.2	NP_001107039.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC75A	ENST00000470794.2	c.376-5045A>G		intron_variant	Intron 2 of 3	1	NM_001113567.3	ENSP00000419502.1

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92154 AN: 151652 Hom.: 28671 Cov.: 30

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.608 AC: 92218 AN: 151774 Hom.: 28693 Cov.: 30 AF XY: 0.603 AC XY: 44692 AN XY: 74132

Gnomad4 AFR AF: 0.594 AC: 0.594489 AN: 0.594489

Gnomad4 AMR AF: 0.535 AC: 0.535077 AN: 0.535077

Gnomad4 ASJ AF: 0.664 AC: 0.66436 AN: 0.66436

Gnomad4 EAS AF: 0.268 AC: 0.267619 AN: 0.267619

Gnomad4 SAS AF: 0.451 AC: 0.450584 AN: 0.450584

Gnomad4 FIN AF: 0.633 AC: 0.633169 AN: 0.633169

Gnomad4 NFE AF: 0.663 AC: 0.663193 AN: 0.663193

Gnomad4 OTH AF: 0.597 AC: 0.597064 AN: 0.597064

Alfa AF: 0.641 Hom.: 3891

Bravo AF: 0.595

Asia WGS AF: 0.368 AC: 1281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.81
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs8082268; hg19: chr17-16356319; COSMIC: COSV69125195; COSMIC: COSV69125195;