rs11189510

Variant names:

• chr10-98202516-G-A
• rs11189510
• NM_001351015.2:c.-14-5585G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
R3HCC1L	NM_001351015.2	c.-14-5585G>A		intron_variant	Intron 4 of 9	ENST00000298999.8	NP_001337944.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
R3HCC1L	ENST00000298999.8	c.-14-5585G>A		intron_variant	Intron 4 of 9	5	NM_001351015.2	ENSP00000298999.3

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

African (AFR) AF: 0.137 AC: 5668 AN: 41430

American (AMR) AF: 0.127 AC: 1933 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0921 AC: 319 AN: 3464

East Asian (EAS) AF: 0.167 AC: 861 AN: 5144

South Asian (SAS) AF: 0.144 AC: 692 AN: 4812

European-Finnish (FIN) AF: 0.116 AC: 1220 AN: 10552

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7847 AN: 67964

Other (OTH) AF: 0.145 AC: 307 AN: 2110

Alfa AF: 0.122 Hom.: 4957

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
PhyloP100		0.18
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

Other links and lift over

dbSNP: rs11189510; hg19: chr10-99962273;