chr5-79874601-T-C

Variant names:

• chr5-79874601-T-C
• rs264986
• XR_948500.3:n.80+14661T>C

Variant summary

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

The XR_948500.3(LOC105379048):​n.80+14661T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,082 control chromosomes in the GnomAD database, including 36,422 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 0.69 (36422 hom., cov: 31)
• Consequence: LOC105379048 XR_948500.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 3 publications found

Genes affected

LOC105379048 (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 (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105059 AN: 151964 Hom.: 36390 Cov.: 31

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.691 AC: 105141 AN: 152082 Hom.: 36422 Cov.: 31 AF XY: 0.695 AC XY: 51698 AN XY: 74354

African (AFR) AF: 0.650 AC: 26952 AN: 41470

American (AMR) AF: 0.726 AC: 11106 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2426 AN: 3468

East Asian (EAS) AF: 0.785 AC: 4059 AN: 5170

South Asian (SAS) AF: 0.694 AC: 3343 AN: 4818

European-Finnish (FIN) AF: 0.701 AC: 7419 AN: 10590

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.703 AC: 47758 AN: 67960

Other (OTH) AF: 0.684 AC: 1446 AN: 2114

Alfa AF: 0.693 Hom.: 6860

Bravo AF: 0.694

Asia WGS AF: 0.714 AC: 2481 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	0.15
DANN	Benign	0.37
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs264986; hg19: chr5-79170424;