rs6782299

chr3-180832914-G-T

Variant summary

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

The NR_109986.1(LOC101928882):n.250+14593C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,190 control chromosomes in the GnomAD database, including 49,579 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 0.80 (49579 hom., cov: 33)
• Consequence: LOC101928882 NR_109986.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995

Genes affected

(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 (AFR) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928882	NR_109986.1	n.250+14593C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000485055.5	n.250+14593C>A		intron_variant, non_coding_transcript_variant		1
	ENST00000495817.1	n.206+37886C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121905 AN: 152074 Hom.: 49528 Cov.: 33

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.802 AC: 122009 AN: 152190 Hom.: 49579 Cov.: 33 AF XY: 0.803 AC XY: 59740 AN XY: 74396

Gnomad4 AFR AF: 0.949

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.757

Alfa AF: 0.741 Hom.: 50642

Bravo AF: 0.809

Asia WGS AF: 0.765 AC: 2664 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	0.21
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6782299; hg19: chr3-180550702;