7-7321892-G-T

Variant names:

• chr7-7321892-G-T
• rs1882600
• XR_002956539.2:n.441+50048G>T

Variant summary

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

The XR_002956539.2(LOC107986764):​n.441+50048G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 152,012 control chromosomes in the GnomAD database, including 23,341 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 0.52 (23341 hom., cov: 32)
• Consequence: LOC107986764 XR_002956539.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.01
• Publications: 3 publications found

Genes affected

LOC107986764 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 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: 0.522 AC: 79230 AN: 151894 Hom.: 23328 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.521 AC: 79261 AN: 152012 Hom.: 23341 Cov.: 32 AF XY: 0.526 AC XY: 39051 AN XY: 74266

African (AFR) AF: 0.224 AC: 9301 AN: 41448

American (AMR) AF: 0.591 AC: 9027 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2387 AN: 3468

East Asian (EAS) AF: 0.734 AC: 3791 AN: 5166

South Asian (SAS) AF: 0.664 AC: 3197 AN: 4816

European-Finnish (FIN) AF: 0.625 AC: 6592 AN: 10554

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43034 AN: 67962

Other (OTH) AF: 0.545 AC: 1148 AN: 2108

Alfa AF: 0.601 Hom.: 27207

Bravo AF: 0.508

Asia WGS AF: 0.690 AC: 2398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.67
PhyloP100		2.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1882600;

hg19: chr7-7361523;