rs9304990

Positions:

• chr19-21658577-A-C
• chr19-21658577-A-T

Variant summary

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

The NR_144514.1(LOC400682):​n.3465A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0827 in 152,154 control chromosomes in the GnomAD database, including 903 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 0.083 (903 hom., cov: 33)
• Consequence: LOC400682 NR_144514.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

Genes affected

LOC400682 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC400682	NR_144514.1	n.3465A>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0827 AC: 12567 AN: 152036 Hom.: 900 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0516

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.00405

Gnomad SAS AF: 0.0515

Gnomad FIN AF: 0.0220

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0437

Gnomad OTH AF: 0.0673

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

GnomAD4 genome AF: 0.0827 AC: 12578 AN: 152154 Hom.: 903 Cov.: 33 AF XY: 0.0797 AC XY: 5929 AN XY: 74400

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.0515

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.00406

Gnomad4 SAS AF: 0.0509

Gnomad4 FIN AF: 0.0220

Gnomad4 NFE AF: 0.0437

Gnomad4 OTH AF: 0.0695

Alfa AF: 0.0503 Hom.: 87

Bravo AF: 0.0885

Asia WGS AF: 0.0520 AC: 183 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.6
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: rs9304990; hg19: chr19-21841379;