rs32249

Variant names:

• chr5-12466863-C-T
• rs32249
• ENST00000830573.1:n.471+63612G>A

Variant summary

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

The NR_188266.1(LOC105374655):​n.365+63612G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.038 in 152,216 control chromosomes in the GnomAD database, including 164 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 0.038 (164 hom., cov: 32)
• Consequence: LOC105374655 NR_188266.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13
• Publications: 3 publications found

Genes affected

ENSG00000248783 (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 (AFR) allele frequency at 95% confidence interval = 0.0627 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188266.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105374655	NR_188266.1		n.365+63612G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248783	ENST00000830573.1		n.471+63612G>A		intron	N/A
	ENSG00000248783	ENST00000830574.1		n.490+63612G>A		intron	N/A
	ENSG00000248783	ENST00000830575.1		n.490+63612G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0380 AC: 5774 AN: 152098 Hom.: 162 Cov.: 32

Gnomad AFR AF: 0.0646

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0335

Gnomad ASJ AF: 0.0553

Gnomad EAS AF: 0.000580

Gnomad SAS AF: 0.0514

Gnomad FIN AF: 0.00650

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0288

Gnomad OTH AF: 0.0383

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

GnomAD4 genome AF: 0.0380 AC: 5785 AN: 152216 Hom.: 164 Cov.: 32 AF XY: 0.0374 AC XY: 2781 AN XY: 74418

African (AFR) AF: 0.0647 AC: 2689 AN: 41530

American (AMR) AF: 0.0334 AC: 511 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0553 AC: 192 AN: 3472

East Asian (EAS) AF: 0.000581 AC: 3 AN: 5164

South Asian (SAS) AF: 0.0517 AC: 249 AN: 4820

European-Finnish (FIN) AF: 0.00650 AC: 69 AN: 10612

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0288 AC: 1959 AN: 68014

Other (OTH) AF: 0.0379 AC: 80 AN: 2112

Alfa AF: 0.0369 Hom.: 24

Bravo AF: 0.0410

Asia WGS AF: 0.0250 AC: 91 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	0.044
DANN	Benign	0.82
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs32249; hg19: chr5-12466975;