chr7-118519495-G-A

Variant names:

• chr7-118519495-G-A
• rs2106595
• XR_927909.2:n.426+5668G>A

Variant summary

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

The XR_927909.2(LOC105375473):​n.426+5668G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 151,250 control chromosomes in the GnomAD database, including 6,120 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 0.26 (6120 hom., cov: 31)
• Consequence: LOC105375473 XR_927909.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586
• Publications: 10 publications found

Genes affected

LOC105375473 (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 = 0.345 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: 0.260 AC: 39232 AN: 151132 Hom.: 6122 Cov.: 31

Gnomad AFR AF: 0.0952

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.259 AC: 39218 AN: 151250 Hom.: 6120 Cov.: 31 AF XY: 0.254 AC XY: 18743 AN XY: 73862

African (AFR) AF: 0.0949 AC: 3901 AN: 41086

American (AMR) AF: 0.276 AC: 4177 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1474 AN: 3458

East Asian (EAS) AF: 0.303 AC: 1545 AN: 5102

South Asian (SAS) AF: 0.210 AC: 1011 AN: 4818

European-Finnish (FIN) AF: 0.223 AC: 2349 AN: 10552

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23606 AN: 67776

Other (OTH) AF: 0.313 AC: 656 AN: 2098

Alfa AF: 0.220 Hom.: 1234

Bravo AF: 0.261

Asia WGS AF: 0.242 AC: 844 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	1.7
DANN	Benign	0.56
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs2106595; hg19: chr7-118159549;