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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379107	XR_001742830.2	n.1444G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105379107	XR_001742831.2	n.1588G>A		non_coding_transcript_exon_variant	Exon 6 of 6
LOC105379107	XR_001742832.1	n.1283G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105379107	XR_001742833.2	n.759+685G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;