8-20705131-G-T

Variant names:

• chr8-20705131-G-T
• rs896044
• XR_949569.4:n.71+40225G>T

Variant summary

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

The XR_949569.4(LOC105379315):​n.71+40225G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,026 control chromosomes in the GnomAD database, including 25,029 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 0.57 (25029 hom., cov: 33)
• Consequence: LOC105379315 XR_949569.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86549 AN: 151908 Hom.: 25008 Cov.: 33

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.570 AC: 86621 AN: 152026 Hom.: 25029 Cov.: 33 AF XY: 0.566 AC XY: 42077 AN XY: 74286

African (AFR) AF: 0.481 AC: 19963 AN: 41460

American (AMR) AF: 0.491 AC: 7506 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2262 AN: 3466

East Asian (EAS) AF: 0.414 AC: 2142 AN: 5174

South Asian (SAS) AF: 0.619 AC: 2977 AN: 4810

European-Finnish (FIN) AF: 0.607 AC: 6400 AN: 10538

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43449 AN: 67964

Other (OTH) AF: 0.580 AC: 1222 AN: 2108

Alfa AF: 0.606 Hom.: 51768

Bravo AF: 0.551

Asia WGS AF: 0.505 AC: 1759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.26
DANN	Benign	0.68
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs896044; hg19: chr8-20562642;