7-108819472-C-T

Variant names:

• chr7-108819472-C-T
• rs1525200
• XR_001745322.1:n.378-21185C>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.378-21185C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 152,066 control chromosomes in the GnomAD database, including 52,707 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 0.80 (52707 hom., cov: 31)
• Consequence: LOC107986836 XR_001745322.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.951 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: 0.797 AC: 121082 AN: 151948 Hom.: 52700 Cov.: 31

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.907

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.955

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.957

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.796 AC: 121105 AN: 152066 Hom.: 52707 Cov.: 31 AF XY: 0.801 AC XY: 59507 AN XY: 74334

African (AFR) AF: 0.407 AC: 16841 AN: 41410

American (AMR) AF: 0.907 AC: 13848 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 3143 AN: 3472

East Asian (EAS) AF: 0.938 AC: 4844 AN: 5164

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

European-Finnish (FIN) AF: 0.927 AC: 9834 AN: 10604

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.957 AC: 65083 AN: 68018

Other (OTH) AF: 0.836 AC: 1760 AN: 2106

Alfa AF: 0.864 Hom.: 7441

Bravo AF: 0.775

Asia WGS AF: 0.898 AC: 3123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.41
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1525200; hg19: chr7-108459916;