rs604096

Variant names:

• chr11-118604383-A-G
• rs604096
• XR_007062908.1:n.3195T>C

Variant summary

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

The XR_007062908.1(LOC124902765):​n.3195T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,110 control chromosomes in the GnomAD database, including 4,840 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 0.25 (4840 hom., cov: 32)
• Consequence: LOC124902765 XR_007062908.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360
• Publications: 8 publications found

Genes affected

LOC124902765 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902765	XR_007062908.1	n.3195T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37810 AN: 151992 Hom.: 4840 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.249 AC: 37832 AN: 152110 Hom.: 4840 Cov.: 32 AF XY: 0.252 AC XY: 18717 AN XY: 74384

African (AFR) AF: 0.276 AC: 11465 AN: 41486

American (AMR) AF: 0.179 AC: 2730 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 848 AN: 3470

East Asian (EAS) AF: 0.336 AC: 1738 AN: 5176

South Asian (SAS) AF: 0.348 AC: 1676 AN: 4822

European-Finnish (FIN) AF: 0.263 AC: 2780 AN: 10572

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15859 AN: 67980

Other (OTH) AF: 0.236 AC: 499 AN: 2112

Alfa AF: 0.232 Hom.: 5816

Bravo AF: 0.240

Asia WGS AF: 0.367 AC: 1279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.94
DANN	Benign	0.47
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs604096; hg19: chr11-118475098;