rs9838229

Positions:

• chr3-180815463-C-A
• chr3-180815463-C-G
• chr3-180815463-C-T

Variant summary

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

The NR_109986.1(LOC101928882):​n.251-4993G>T 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 0.798 in 152,190 control chromosomes in the GnomAD database, including 49,064 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 (49064 hom., cov: 33)
• Consequence: LOC101928882 NR_109986.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928882	NR_109986.1	n.251-4993G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000485055.5	n.251-4993G>T		intron_variant, non_coding_transcript_variant		1
	ENST00000495817.1	n.207-33339G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121338 AN: 152072 Hom.: 49020 Cov.: 33

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.798 AC: 121436 AN: 152190 Hom.: 49064 Cov.: 33 AF XY: 0.799 AC XY: 59480 AN XY: 74414

Gnomad4 AFR AF: 0.937

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.853

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.753

Alfa AF: 0.731 Hom.: 78660

Bravo AF: 0.805

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.53
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9838229; hg19: chr3-180533251;