XR_948633.2:n.277+767T>C

Variant names:

• chr5-103068317-A-G
• rs34374
• XR_948633.2:n.277+767T>C

Variant summary

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

The XR_948633.2(LOC105379105):​n.277+767T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 152,146 control chromosomes in the GnomAD database, including 17,048 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 0.45 (17048 hom., cov: 33)
• Consequence: LOC105379105 XR_948633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 8 publications found

Genes affected

LOC105379105 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 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: 0.451 AC: 68519 AN: 152028 Hom.: 16998 Cov.: 33

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.451 AC: 68627 AN: 152146 Hom.: 17048 Cov.: 33 AF XY: 0.446 AC XY: 33187 AN XY: 74394

African (AFR) AF: 0.670 AC: 27807 AN: 41496

American (AMR) AF: 0.417 AC: 6372 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1054 AN: 3470

East Asian (EAS) AF: 0.499 AC: 2586 AN: 5180

South Asian (SAS) AF: 0.250 AC: 1207 AN: 4822

European-Finnish (FIN) AF: 0.344 AC: 3641 AN: 10590

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24599 AN: 67990

Other (OTH) AF: 0.408 AC: 861 AN: 2112

Alfa AF: 0.382 Hom.: 6783

Bravo AF: 0.467

Asia WGS AF: 0.384 AC: 1333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.92
DANN	Benign	0.39
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs34374; hg19: chr5-102404021; COSMIC: COSV60175258;