XR_949569.4:n.182+51973C>G

Variant names:

• chr8-20842529-C-G
• rs2927385
• XR_949569.4:n.182+51973C>G

Variant summary

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

The XR_949569.4(LOC105379315):​n.182+51973C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 151,998 control chromosomes in the GnomAD database, including 33,509 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 0.65 (33509 hom., cov: 31)
• Consequence: LOC105379315 XR_949569.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 5 publications found

Genes affected

LOC105379315 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379315	XR_949569.4	n.182+51973C>G		intron_variant	Intron 2 of 6

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98074 AN: 151880 Hom.: 33455 Cov.: 31

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.646 AC: 98181 AN: 151998 Hom.: 33509 Cov.: 31 AF XY: 0.638 AC XY: 47397 AN XY: 74270

African (AFR) AF: 0.864 AC: 35861 AN: 41492

American (AMR) AF: 0.602 AC: 9186 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1973 AN: 3472

East Asian (EAS) AF: 0.237 AC: 1222 AN: 5160

South Asian (SAS) AF: 0.616 AC: 2965 AN: 4810

European-Finnish (FIN) AF: 0.500 AC: 5253 AN: 10512

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39816 AN: 67970

Other (OTH) AF: 0.628 AC: 1326 AN: 2110

Alfa AF: 0.410 Hom.: 796

Bravo AF: 0.659

Asia WGS AF: 0.490 AC: 1708 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	0.29
DANN	Benign	0.35
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2927385; hg19: chr8-20700040;