rs16902947

chr5-36308995-A-G

Variant summary

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

The XR_007058733.1(LOC124900962):n.128-18649A>G 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 0.213 in 152,050 control chromosomes in the GnomAD database, including 3,744 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 0.21 (3744 hom., cov: 32)
• Consequence: LOC124900962 XR_007058733.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

Genes affected

LOC124900962 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900962	XR_007058733.1	n.128-18649A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32388 AN: 151932 Hom.: 3739 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.0243

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.213 AC: 32429 AN: 152050 Hom.: 3744 Cov.: 32 AF XY: 0.216 AC XY: 16025 AN XY: 74312

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.0241

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.227

Alfa AF: 0.189 Hom.: 5771

Bravo AF: 0.207

Asia WGS AF: 0.203 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.1
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16902947; hg19: chr5-36309097;