12-53765493-G-A

Position:

• chr12-53765493-G-A

Variant summary

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

The ENST00000663306.1(ENSG00000286069):​n.278+25605G>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 0.225 in 152,016 control chromosomes in the GnomAD database, including 4,420 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 0.23 (4420 hom., cov: 32)
• Consequence: ENST00000663306.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000663306.1	n.278+25605G>A		intron_variant, non_coding_transcript_variant
	ENST00000652339.1	n.213+25605G>A		intron_variant, non_coding_transcript_variant
	ENST00000654713.1	n.214+25605G>A		intron_variant, non_coding_transcript_variant
	ENST00000656247.1	n.143+14503G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34184 AN: 151898 Hom.: 4416 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0712

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.225 AC: 34216 AN: 152016 Hom.: 4420 Cov.: 32 AF XY: 0.218 AC XY: 16175 AN XY: 74336

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.0714

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.210

Alfa AF: 0.199 Hom.: 6818

Bravo AF: 0.240

Asia WGS AF: 0.116 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.020
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7969151; hg19: chr12-54159277;