NR_105018.1:n.248-50618A>G

Variant names:

• chr5-87193328-A-G
• rs10491362
• NR_105018.1:n.248-50618A>G

Variant summary

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

The NR_105018.1(LOC101929380):​n.248-50618A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0916 in 151,998 control chromosomes in the GnomAD database, including 1,116 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 0.092 (1116 hom., cov: 32)
• Consequence: LOC101929380 NR_105018.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.369
• Publications: 2 publications found

Genes affected

LOC101929380 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929380	NR_105018.1	n.248-50618A>G		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0917 AC: 13922 AN: 151880 Hom.: 1117 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0531

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.0866

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0344

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.0916 AC: 13923 AN: 151998 Hom.: 1116 Cov.: 32 AF XY: 0.0943 AC XY: 7007 AN XY: 74298

African (AFR) AF: 0.163 AC: 6760 AN: 41452

American (AMR) AF: 0.0602 AC: 920 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0531 AC: 184 AN: 3468

East Asian (EAS) AF: 0.377 AC: 1944 AN: 5162

South Asian (SAS) AF: 0.0856 AC: 412 AN: 4812

European-Finnish (FIN) AF: 0.105 AC: 1112 AN: 10566

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0344 AC: 2339 AN: 67956

Other (OTH) AF: 0.0918 AC: 193 AN: 2102

Alfa AF: 0.0624 Hom.: 56

Bravo AF: 0.0939

Asia WGS AF: 0.186 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.9
DANN	Benign	0.53
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs10491362; hg19: chr5-86489145; COSMIC: COSV60165925;