12-71053009-T-C

Position:

• chr12-71053009-T-C

Variant summary

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

The ENST00000548497.1(ENSG00000257454):​n.354-6268A>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 0.226 in 152,166 control chromosomes in the GnomAD database, including 5,035 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 (5035 hom., cov: 32)
• Consequence: ENST00000548497.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.329 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
	ENST00000548497.1	n.354-6268A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000549357.1	n.288-5330A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34343 AN: 152048 Hom.: 5034 Cov.: 32

Gnomad AFR AF: 0.0786

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.00791

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.226 AC: 34348 AN: 152166 Hom.: 5035 Cov.: 32 AF XY: 0.222 AC XY: 16488 AN XY: 74384

Gnomad4 AFR AF: 0.0784

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.00792

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.209

Alfa AF: 0.282 Hom.: 1498

Bravo AF: 0.206

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4760786; hg19: chr12-71446789;