chr12-24770561-C-T

Variant names:

• chr12-24770561-C-T
• rs12305319
• XM_047429950.1:c.243+3335C>T

Variant summary

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

The XM_047429950.1(LOC124902897):​c.243+3335C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0962 in 151,952 control chromosomes in the GnomAD database, including 946 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 0.096 (946 hom., cov: 32)
• Consequence: LOC124902897 XM_047429950.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356

Genes affected

LOC124902897 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902897	XM_047429950.1	c.243+3335C>T		intron_variant	Intron 3 of 3		XP_047285906.1
LOC124902897	XR_007063242.1	n.459-899C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255745	ENST00000536131.1	n.427+3335C>T		intron_variant	Intron 4 of 4	3
ENSG00000255745	ENST00000653796.1	n.425-899C>T		intron_variant	Intron 3 of 4
ENSG00000255745	ENST00000654709.1	n.484+3335C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0962 AC: 14601 AN: 151834 Hom.: 943 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0488

Gnomad EAS AF: 0.0732

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.0522

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0601

Gnomad OTH AF: 0.0925

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

GnomAD4 genome AF: 0.0962 AC: 14625 AN: 151952 Hom.: 946 Cov.: 32 AF XY: 0.0952 AC XY: 7072 AN XY: 74296

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0488

Gnomad4 EAS AF: 0.0728

Gnomad4 SAS AF: 0.0569

Gnomad4 FIN AF: 0.0522

Gnomad4 NFE AF: 0.0601

Gnomad4 OTH AF: 0.0920

Alfa AF: 0.0822 Hom.: 82

Bravo AF: 0.104

Asia WGS AF: 0.0880 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12305319; hg19: chr12-24923495;