7-10110349-C-G

Variant names:

• chr7-10110349-C-G
• rs7778619
• XR_001745088.2:n.101-10125G>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001745088.2(LOC105375149):​n.101-10125G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151,936 control chromosomes in the GnomAD database, including 10,193 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 0.28 (10193 hom., cov: 32)
• Consequence: LOC105375149 XR_001745088.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.11
• Publications: 3 publications found

Genes affected

LOC105375149 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 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: 0.277 AC: 42056 AN: 151820 Hom.: 10147 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.277 AC: 42161 AN: 151936 Hom.: 10193 Cov.: 32 AF XY: 0.280 AC XY: 20781 AN XY: 74240

African (AFR) AF: 0.654 AC: 27098 AN: 41420

American (AMR) AF: 0.158 AC: 2413 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3468

East Asian (EAS) AF: 0.210 AC: 1084 AN: 5154

South Asian (SAS) AF: 0.275 AC: 1324 AN: 4814

European-Finnish (FIN) AF: 0.190 AC: 2008 AN: 10548

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.107 AC: 7240 AN: 67960

Other (OTH) AF: 0.227 AC: 479 AN: 2110

Alfa AF: 0.0675 Hom.: 105

Bravo AF: 0.288

Asia WGS AF: 0.308 AC: 1075 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	18
DANN	Benign	0.70
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs7778619; hg19: chr7-10149976;