chr7-7315484-G-C

Variant names:

• chr7-7315484-G-C
• rs719423
• XR_002956539.2:n.441+43640G>C

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+43640G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,982 control chromosomes in the GnomAD database, including 17,882 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 0.48 (17882 hom., cov: 32)
• Consequence: LOC107986764 XR_002956539.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.790
• Publications: 4 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 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: 0.476 AC: 72316 AN: 151864 Hom.: 17866 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.476 AC: 72374 AN: 151982 Hom.: 17882 Cov.: 32 AF XY: 0.482 AC XY: 35775 AN XY: 74298

African (AFR) AF: 0.562 AC: 23273 AN: 41430

American (AMR) AF: 0.542 AC: 8288 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1874 AN: 3468

East Asian (EAS) AF: 0.702 AC: 3619 AN: 5158

South Asian (SAS) AF: 0.543 AC: 2610 AN: 4810

European-Finnish (FIN) AF: 0.415 AC: 4375 AN: 10542

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26790 AN: 67964

Other (OTH) AF: 0.482 AC: 1016 AN: 2108

Alfa AF: 0.437 Hom.: 1876

Bravo AF: 0.490

Asia WGS AF: 0.611 AC: 2126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.72
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs719423; hg19: chr7-7355115;