rs287644

Variant names:

• chr5-114673592-G-A
• rs287644
• NR_130785.1:n.80-5361C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-114673592-G-A
• chr5-114673592-G-T

Variant summary

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

The NR_130785.1(LOC101927078):​n.80-5361C>T variant causes a intron change. The variant allele was found at a frequency of 0.119 in 151,560 control chromosomes in the GnomAD database, including 1,389 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 0.12 (1389 hom., cov: 31)
• Consequence: LOC101927078 NR_130785.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 0 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) 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.80-5361C>T		intron_variant	Intron 1 of 12

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.119 AC: 17970 AN: 151442 Hom.: 1388 Cov.: 31

Gnomad AFR AF: 0.0351

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.0769

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.119 AC: 17969 AN: 151560 Hom.: 1389 Cov.: 31 AF XY: 0.120 AC XY: 8853 AN XY: 74038

African (AFR) AF: 0.0350 AC: 1449 AN: 41344

American (AMR) AF: 0.117 AC: 1778 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 417 AN: 3462

East Asian (EAS) AF: 0.193 AC: 989 AN: 5134

South Asian (SAS) AF: 0.0775 AC: 373 AN: 4810

European-Finnish (FIN) AF: 0.191 AC: 2010 AN: 10506

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10560 AN: 67768

Other (OTH) AF: 0.119 AC: 249 AN: 2100

Alfa AF: 0.0493 Hom.: 47

Bravo AF: 0.113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.3
DANN	Benign	0.83

Splicing

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

Other links and lift over

dbSNP: rs287644; hg19: chr5-114009289;