3-86206522-T-C

Variant names:

• chr3-86206522-T-C
• rs7428796
• NR_188544.1:n.680-589A>G

Variant summary

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

The NR_188544.1(LOC102723364):​n.680-589A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,556 control chromosomes in the GnomAD database, including 20,761 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 0.51 (20761 hom., cov: 29)
• Consequence: LOC102723364 NR_188544.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

Genes affected

LOC102723364 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723364	NR_188544.1	n.680-589A>G		intron_variant	Intron 4 of 4
LOC102723364	NR_188545.1	n.598-589A>G		intron_variant	Intron 3 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76636 AN: 151440 Hom.: 20760 Cov.: 29

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.506 AC: 76661 AN: 151556 Hom.: 20761 Cov.: 29 AF XY: 0.504 AC XY: 37315 AN XY: 74050

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.522

Alfa AF: 0.590 Hom.: 36364

Bravo AF: 0.489

Asia WGS AF: 0.439 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7428796; hg19: chr3-86255672;