7-108824307-C-T

Variant names:

• chr7-108824307-C-T
• rs7781585
• XR_001745322.1:n.378-16350C>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.378-16350C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 152,154 control chromosomes in the GnomAD database, including 56,093 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 0.84 (56093 hom., cov: 33)
• Consequence: LOC107986836 XR_001745322.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.952 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: 0.840 AC: 127762 AN: 152036 Hom.: 56085 Cov.: 33

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.955

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.840 AC: 127806 AN: 152154 Hom.: 56093 Cov.: 33 AF XY: 0.843 AC XY: 62685 AN XY: 74392

African (AFR) AF: 0.555 AC: 23028 AN: 41472

American (AMR) AF: 0.926 AC: 14130 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.924 AC: 3205 AN: 3468

East Asian (EAS) AF: 0.938 AC: 4846 AN: 5168

South Asian (SAS) AF: 0.955 AC: 4611 AN: 4830

European-Finnish (FIN) AF: 0.927 AC: 9836 AN: 10608

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.958 AC: 65164 AN: 68024

Other (OTH) AF: 0.868 AC: 1834 AN: 2114

Alfa AF: 0.878 Hom.: 7844

Bravo AF: 0.825

Asia WGS AF: 0.912 AC: 3166 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.34
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs7781585; hg19: chr7-108464751;