XR_001742568.1:n.910A>G

Variant names:

• chr5-4831488-T-C
• rs816475
• XR_001742568.1:n.910A>G

Variant summary

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

The XR_001742568.1(LOC107986400):​n.910A>G 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 0.239 in 151,976 control chromosomes in the GnomAD database, including 6,895 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 0.24 (6895 hom., cov: 32)
• Consequence: LOC107986400 XR_001742568.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 5 publications found

Genes affected

LOC107986400 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986400	XR_001742568.1	n.910A>G		non_coding_transcript_exon_variant	Exon 4 of 4
LOC107986400	XR_001742571.1	n.851A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LOC107986400	XR_001742577.1	n.760A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248973	ENST00000506059.2	n.215-25640A>G		intron_variant	Intron 2 of 3	3
ENSG00000248973	ENST00000507435.1	n.207-25640A>G		intron_variant	Intron 1 of 5	5
ENSG00000248973	ENST00000651493.1	n.369+10185A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36288 AN: 151858 Hom.: 6865 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0784

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.239 AC: 36381 AN: 151976 Hom.: 6895 Cov.: 32 AF XY: 0.237 AC XY: 17571 AN XY: 74292

African (AFR) AF: 0.520 AC: 21544 AN: 41426

American (AMR) AF: 0.261 AC: 3991 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3468

East Asian (EAS) AF: 0.115 AC: 593 AN: 5156

South Asian (SAS) AF: 0.191 AC: 920 AN: 4814

European-Finnish (FIN) AF: 0.0784 AC: 830 AN: 10592

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.107 AC: 7276 AN: 67946

Other (OTH) AF: 0.226 AC: 475 AN: 2098

Alfa AF: 0.138 Hom.: 3195

Bravo AF: 0.266

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.063
DANN	Benign	0.63
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs816475; hg19: chr5-4831601;