rs11189510

chr10-98202516-G-A

Variant summary

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

The NM_001351015.2(R3HCC1L):c.-14-5585G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 151,960 control chromosomes in the GnomAD database, including 1,235 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 0.13 (1235 hom., cov: 31)
• Consequence: R3HCC1L NM_001351015.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182

Genes affected

R3HCC1L (HGNC:23512): (R3H domain and coiled-coil containing 1 like) Colocalizes with exon-exon junction complex. [provided by Alliance of Genome Resources, Apr 2022]

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 (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
R3HCC1L	NM_001351015.2	c.-14-5585G>A		intron_variant		ENST00000298999.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
R3HCC1L	ENST00000298999.8	c.-14-5585G>A		intron_variant		5	NM_001351015.2	P2

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19002 AN: 151842 Hom.: 1235 Cov.: 31

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0921

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.125 AC: 19023 AN: 151960 Hom.: 1235 Cov.: 31 AF XY: 0.127 AC XY: 9399 AN XY: 74280

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.0921

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.145

Alfa AF: 0.122 Hom.: 2425

Bravo AF: 0.125

Asia WGS AF: 0.153 AC: 533 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	2.3
Dann	Benign	0.71

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: rs11189510; hg19: chr10-99962273;