rs12771728

chr10-87595556-T-C

Variant summary

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

The ENST00000446794.1(ENSG00000223761):n.32-3813A>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 0.279 in 152,066 control chromosomes in the GnomAD database, including 6,571 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 0.28 (6571 hom., cov: 32)
• Consequence: ENST00000446794.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204

Genes affected

(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 (NFE) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000446794.1	n.32-3813A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42471 AN: 151948 Hom.: 6567 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.279 AC: 42500 AN: 152066 Hom.: 6571 Cov.: 32 AF XY: 0.276 AC XY: 20484 AN XY: 74338

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.288

Alfa AF: 0.339 Hom.: 18374

Bravo AF: 0.272

Asia WGS AF: 0.281 AC: 974 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.4
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: rs12771728; hg19: chr10-89355313;