rs7703891

Variant names:

• chr5-114696777-T-C
• rs7703891
• NR_130785.1:n.80-28546A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-114696777-T-C
• chr5-114696777-T-G

Variant summary

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

The NR_130785.1(LOC101927078):​n.80-28546A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0794 in 152,232 control chromosomes in the GnomAD database, including 849 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 0.079 (849 hom., cov: 33)
• Consequence: LOC101927078 NR_130785.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 1 publications found

Genes affected

LOC101927078 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927078	NR_130785.1	n.80-28546A>G		intron_variant	Intron 1 of 12

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0792 AC: 12053 AN: 152114 Hom.: 846 Cov.: 33

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0444

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0176

Gnomad FIN AF: 0.0332

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0417

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0794 AC: 12080 AN: 152232 Hom.: 849 Cov.: 33 AF XY: 0.0760 AC XY: 5661 AN XY: 74460

African (AFR) AF: 0.186 AC: 7720 AN: 41498

American (AMR) AF: 0.0444 AC: 679 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.0182 AC: 88 AN: 4826

European-Finnish (FIN) AF: 0.0332 AC: 353 AN: 10618

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0417 AC: 2837 AN: 68022

Other (OTH) AF: 0.0681 AC: 144 AN: 2114

Alfa AF: 0.0207 Hom.: 28

Bravo AF: 0.0867

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7703891; hg19: chr5-114032474;