rs8082268

chr17-16453005-T-C

Variant summary

Our verdict is Benign. Variant got -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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LRRC75A	NM_001113567.3	c.376-5045A>G		intron_variant		ENST00000470794.2
SNHG29	NR_027171.1	n.554+11875T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC75A	ENST00000470794.2	c.376-5045A>G		intron_variant		1	NM_001113567.3	P1
SNHG29	ENST00000702366.1	n.238+11875T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.597

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

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;