rs4703272

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001742831.2(LOC105379107):​n.1588G>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_001742831.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.892

Genes affected

LOC105379107 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105379107	XR_001742831.2	n.1588G>A		non_coding_transcript_exon_variant	6/6
LOC105379107	XR_001742830.2	n.1444G>A		non_coding_transcript_exon_variant	3/3
LOC105379107	XR_001742832.1	n.1283G>A		non_coding_transcript_exon_variant	3/3
LOC105379107	XR_001742833.2	n.759+685G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.748

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.666

Alfa AF: 0.714 Hom.: 34785

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4703272; hg19: chr5-103270358;