chr9-111624319-C-T

Variant names:

• chr9-111624319-C-T
• rs10121085
• ENST00000374304.1:n.250+6721G>A

Variant summary

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

The ENST00000374304.1(LRRC37A5P):​n.250+6721G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 151,266 control chromosomes in the GnomAD database, including 988 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 0.11 (988 hom., cov: 31)
• Consequence: LRRC37A5P ENST00000374304.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665
• Publications: 1 publications found

Genes affected

LRRC37A5P (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000374304.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC37A5P	ENST00000374304.1	TSL:1	n.250+6721G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16361 AN: 151208 Hom.: 987 Cov.: 31

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0875

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0559

Gnomad MID AF: 0.157

Gnomad NFE AF: 0.0809

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.108 AC: 16369 AN: 151266 Hom.: 988 Cov.: 31 AF XY: 0.109 AC XY: 8054 AN XY: 73808

African (AFR) AF: 0.154 AC: 6326 AN: 41154

American (AMR) AF: 0.110 AC: 1662 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.0875 AC: 303 AN: 3462

East Asian (EAS) AF: 0.153 AC: 786 AN: 5126

South Asian (SAS) AF: 0.162 AC: 775 AN: 4790

European-Finnish (FIN) AF: 0.0559 AC: 576 AN: 10302

Middle Eastern (MID) AF: 0.150 AC: 43 AN: 286

European-Non Finnish (NFE) AF: 0.0809 AC: 5497 AN: 67964

Other (OTH) AF: 0.122 AC: 256 AN: 2094

Alfa AF: 0.0916 Hom.: 2616

Bravo AF: 0.112

Asia WGS AF: 0.176 AC: 612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.82
DANN	Benign	0.62
PhyloP100		-0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10121085; hg19: chr9-114386599;