7-108826397-A-T

Variant names:

• chr7-108826397-A-T
• rs1568855
• XR_001745322.1:n.378-14260A>T

Variant summary

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

The XR_001745322.1(LOC107986836):​n.378-14260A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.901 in 152,202 control chromosomes in the GnomAD database, including 62,375 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 0.90 (62375 hom., cov: 33)
• Consequence: LOC107986836 XR_001745322.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 1 publications found

Genes affected

LOC107986836 (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 = 0.953 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: 0.901 AC: 137094 AN: 152084 Hom.: 62346 Cov.: 33

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.956

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.959

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.901 AC: 137176 AN: 152202 Hom.: 62375 Cov.: 33 AF XY: 0.901 AC XY: 67059 AN XY: 74420

African (AFR) AF: 0.767 AC: 31820 AN: 41502

American (AMR) AF: 0.951 AC: 14534 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.924 AC: 3208 AN: 3472

East Asian (EAS) AF: 0.938 AC: 4848 AN: 5170

South Asian (SAS) AF: 0.955 AC: 4607 AN: 4822

European-Finnish (FIN) AF: 0.927 AC: 9838 AN: 10612

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.959 AC: 65245 AN: 68024

Other (OTH) AF: 0.909 AC: 1919 AN: 2112

Alfa AF: 0.929 Hom.: 8201

Bravo AF: 0.896

Asia WGS AF: 0.931 AC: 3235 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.70
DANN	Benign	0.49
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1568855; hg19: chr7-108466841;