rs7319358

Variant names:

• chr13-78976799-C-T
• rs7319358
• XR_942108.4:n.276+2846G>A

Variant summary

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

The XR_942108.4(LOC105370273):​n.276+2846G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,092 control chromosomes in the GnomAD database, including 9,780 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 0.34 (9780 hom., cov: 32)
• Consequence: LOC105370273 XR_942108.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 9 publications found

Genes affected

LOC105370273 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.436 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: 0.342 AC: 52035 AN: 151974 Hom.: 9775 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.342 AC: 52044 AN: 152092 Hom.: 9780 Cov.: 32 AF XY: 0.336 AC XY: 24980 AN XY: 74324

African (AFR) AF: 0.182 AC: 7553 AN: 41502

American (AMR) AF: 0.369 AC: 5643 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1340 AN: 3468

East Asian (EAS) AF: 0.226 AC: 1166 AN: 5164

South Asian (SAS) AF: 0.452 AC: 2175 AN: 4816

European-Finnish (FIN) AF: 0.324 AC: 3433 AN: 10586

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.434 AC: 29492 AN: 67972

Other (OTH) AF: 0.368 AC: 776 AN: 2108

Alfa AF: 0.394 Hom.: 27648

Bravo AF: 0.332

Asia WGS AF: 0.357 AC: 1241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.46
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs7319358; hg19: chr13-79550934;