rs3865444

Positions:

• chr19-51224706-C-A

Variant summary

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

The XR_007067309.1(LOC107985327):​n.232-30046G>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 0.254 in 152,044 control chromosomes in the GnomAD database, including 6,038 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 0.25 (6038 hom., cov: 31)
• Consequence: LOC107985327 XR_007067309.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

Genes affected

LOC107985327 (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 (AMR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985327	XR_007067309.1	n.232-30046G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38556 AN: 151926 Hom.: 6026 Cov.: 31

Gnomad AFR AF: 0.0868

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.254 AC: 38576 AN: 152044 Hom.: 6038 Cov.: 31 AF XY: 0.258 AC XY: 19175 AN XY: 74316

Gnomad4 AFR AF: 0.0868

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.250

Alfa AF: 0.302 Hom.: 16394

Bravo AF: 0.255

Asia WGS AF: 0.170 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.25
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3865444; hg19: chr19-51727962;