rs2645444

Variant names:

• chr8-11794044-C-T
• rs2645444
• XR_948962.4:n.44-5977G>A

Variant summary

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

The XR_948962.4(LOC105379243):​n.44-5977G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 151,998 control chromosomes in the GnomAD database, including 50,632 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 0.81 (50632 hom., cov: 31)
• Consequence: LOC105379243 XR_948962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.897
• Publications: 8 publications found

Genes affected

LOC105379243 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379243	XR_948962.4	n.44-5977G>A		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.815 AC: 123715 AN: 151880 Hom.: 50578 Cov.: 31

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.815 AC: 123827 AN: 151998 Hom.: 50632 Cov.: 31 AF XY: 0.819 AC XY: 60835 AN XY: 74294

African (AFR) AF: 0.779 AC: 32254 AN: 41414

American (AMR) AF: 0.873 AC: 13348 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2597 AN: 3470

East Asian (EAS) AF: 0.996 AC: 5146 AN: 5168

South Asian (SAS) AF: 0.844 AC: 4069 AN: 4820

European-Finnish (FIN) AF: 0.836 AC: 8835 AN: 10570

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 54962 AN: 67966

Other (OTH) AF: 0.821 AC: 1727 AN: 2104

Alfa AF: 0.814 Hom.: 87025

Bravo AF: 0.815

Asia WGS AF: 0.925 AC: 3212 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	0.37
DANN	Benign	0.25
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs2645444; hg19: chr8-11651553;