5-36308995-A-G

Variant names:

• chr5-36308995-A-G
• rs16902947
• XR_007058733.1:n.128-18649A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007058733.1(LOC124900962):​n.128-18649A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 5 publications found

Genes affected

LOC124900962 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.288 AC: 11949 AN: 41456

American (AMR) AF: 0.153 AC: 2340 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 698 AN: 3472

East Asian (EAS) AF: 0.0241 AC: 125 AN: 5180

South Asian (SAS) AF: 0.292 AC: 1406 AN: 4812

European-Finnish (FIN) AF: 0.236 AC: 2493 AN: 10576

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12591 AN: 67970

Other (OTH) AF: 0.227 AC: 480 AN: 2116

Alfa AF: 0.192 Hom.: 13053

Bravo AF: 0.207

Asia WGS AF: 0.203 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.56
PhyloP100		-0.071

Splicing

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

Other links and lift over

dbSNP: rs16902947; hg19: chr5-36309097;