3-129533079-A-T

Position:

• chr3-129533079-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000539.3(RHO):​c.936+307A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,038 control chromosomes in the GnomAD database, including 17,322 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 0.37 (17322 hom., cov: 32)
• Consequence: RHO NM_000539.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113

Genes affected

RHO (HGNC:10012): (rhodopsin) The protein encoded by this gene is found in rod cells in the back of the eye and is essential for vision in low-light conditions. The encoded protein binds to 11-cis retinal and is activated when light hits the retinal molecule. Defects in this gene are a cause of congenital stationary night blindness. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RHO	NM_000539.3	c.936+307A>T		intron_variant		ENST00000296271.4	NP_000530.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RHO	ENST00000296271.4	c.936+307A>T		intron_variant		1	NM_000539.3	ENSP00000296271.3

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56868 AN: 151918 Hom.: 17261 Cov.: 32

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.0704

Gnomad MID AF: 0.279

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.375 AC: 56990 AN: 152038 Hom.: 17322 Cov.: 32 AF XY: 0.375 AC XY: 27859 AN XY: 74310

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.0704

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.342

Alfa AF: 0.247 Hom.: 1092

Bravo AF: 0.412

Asia WGS AF: 0.499 AC: 1738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.64
DANN	Benign	0.49

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: rs2855557; hg19: chr3-129251922;