8-25781517-A-T

Variant names:

• chr8-25781517-A-T
• rs4872354
• XR_001745849.2:n.239-54861A>T

Variant summary

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

The XR_001745849.2(LOC107986933):​n.239-54861A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,106 control chromosomes in the GnomAD database, including 3,389 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 0.20 (3389 hom., cov: 32)
• Consequence: LOC107986933 XR_001745849.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 5 publications found

Genes affected

LOC107986933 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986933	XR_001745849.2	n.239-54861A>T		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29897 AN: 151988 Hom.: 3377 Cov.: 32

Gnomad AFR AF: 0.0811

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.197 AC: 29925 AN: 152106 Hom.: 3389 Cov.: 32 AF XY: 0.194 AC XY: 14447 AN XY: 74348

African (AFR) AF: 0.0810 AC: 3365 AN: 41528

American (AMR) AF: 0.247 AC: 3770 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3466

East Asian (EAS) AF: 0.205 AC: 1058 AN: 5168

South Asian (SAS) AF: 0.148 AC: 716 AN: 4824

European-Finnish (FIN) AF: 0.238 AC: 2522 AN: 10584

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17178 AN: 67950

Other (OTH) AF: 0.197 AC: 415 AN: 2108

Alfa AF: 0.223 Hom.: 524

Bravo AF: 0.194

Asia WGS AF: 0.212 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.60
DANN	Benign	0.73
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4872354; hg19: chr8-25639033;