rs4703272

Variant names:

• chr5-103934657-G-A
• rs4703272
• XR_001742830.2:n.1444G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-103934657-G-A
• chr5-103934657-G-T

Variant summary

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

The XR_001742830.2(LOC105379107):​n.1444G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 152,068 control chromosomes in the GnomAD database, including 32,843 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 0.64 (32843 hom., cov: 31)
• Consequence: LOC105379107 XR_001742830.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.892
• Publications: 1 publications found

Genes affected

LOC105379107 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.729 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: 0.636 AC: 96690 AN: 151950 Hom.: 32825 Cov.: 31

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.636 AC: 96742 AN: 152068 Hom.: 32843 Cov.: 31 AF XY: 0.642 AC XY: 47723 AN XY: 74326

African (AFR) AF: 0.379 AC: 15699 AN: 41436

American (AMR) AF: 0.673 AC: 10293 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2547 AN: 3472

East Asian (EAS) AF: 0.721 AC: 3722 AN: 5162

South Asian (SAS) AF: 0.748 AC: 3612 AN: 4826

European-Finnish (FIN) AF: 0.817 AC: 8649 AN: 10586

Middle Eastern (MID) AF: 0.747 AC: 218 AN: 292

European-Non Finnish (NFE) AF: 0.735 AC: 49956 AN: 67984

Other (OTH) AF: 0.666 AC: 1407 AN: 2114

Alfa AF: 0.709 Hom.: 39735

Bravo AF: 0.614

Asia WGS AF: 0.736 AC: 2557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.7
DANN	Benign	0.64
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs4703272; hg19: chr5-103270358;