rs10506318

Positions:

• chr12-53794398-T-G

Variant summary

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

The ENST00000663306.1(ENSG00000286069):​n.279-54461T>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 0.104 in 152,212 control chromosomes in the GnomAD database, including 2,504 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 0.10 (2504 hom., cov: 32)
• Consequence: ENST00000663306.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.733

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984525	XR_002957415.2	n.250+24434T>G		intron_variant, non_coding_transcript_variant
LOC107984525	XR_007063320.1	n.27+21758T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663306.1	n.279-54461T>G		intron_variant, non_coding_transcript_variant
	ENST00000652339.1	n.214-54461T>G		intron_variant, non_coding_transcript_variant
	ENST00000654713.1	n.214+54510T>G		intron_variant, non_coding_transcript_variant
	ENST00000656247.1	n.143+43408T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15795 AN: 152094 Hom.: 2492 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00994

Gnomad FIN AF: 0.00254

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.00915

Gnomad OTH AF: 0.0850

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

GnomAD4 genome AF: 0.104 AC: 15844 AN: 152212 Hom.: 2504 Cov.: 32 AF XY: 0.101 AC XY: 7481 AN XY: 74432

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.0417

Gnomad4 ASJ AF: 0.0326

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00974

Gnomad4 FIN AF: 0.00254

Gnomad4 NFE AF: 0.00915

Gnomad4 OTH AF: 0.0841

Alfa AF: 0.0644 Hom.: 194

Bravo AF: 0.118

Asia WGS AF: 0.0240 AC: 86 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.8
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506318; hg19: chr12-54188182;