rs32249

Positions:

• chr5-12466863-C-T

Variant summary

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

The XR_925792.3(LOC105374655):​n.522+63612G>A 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 0.038 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 XR_925792.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13

Genes affected

LOC105374655 (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 (AFR) allele frequency at 95% confidence interval = 0.0627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374655	XR_925792.3	n.522+63612G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.0647

Gnomad4 AMR AF: 0.0334

Gnomad4 ASJ AF: 0.0553

Gnomad4 EAS AF: 0.000581

Gnomad4 SAS AF: 0.0517

Gnomad4 FIN AF: 0.00650

Gnomad4 NFE AF: 0.0288

Gnomad4 OTH AF: 0.0379

Alfa AF: 0.0357 Hom.: 18

Bravo AF: 0.0410

Asia WGS AF: 0.0250 AC: 91 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	0.044
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs32249; hg19: chr5-12466975;