rs12771728

Variant names:

• chr10-87595556-T-C
• rs12771728
• ENST00000446794.1:n.32-3813A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000446794.1(ENSG00000223761):​n.32-3813A>G variant causes a intron 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: ENSG00000223761 ENST00000446794.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204
• Publications: 3 publications found

Genes affected

ENSG00000223761 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223761	ENST00000446794.1	n.32-3813A>G		intron_variant	Intron 1 of 1	3
ENSG00000225913	ENST00000804457.1	n.103-10745T>C		intron_variant	Intron 1 of 4
ENSG00000223761	ENST00000804693.1	n.74+1632A>G		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.167 AC: 6910 AN: 41500

American (AMR) AF: 0.256 AC: 3903 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 976 AN: 3466

East Asian (EAS) AF: 0.192 AC: 994 AN: 5176

South Asian (SAS) AF: 0.309 AC: 1486 AN: 4806

European-Finnish (FIN) AF: 0.284 AC: 3003 AN: 10568

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24211 AN: 67964

Other (OTH) AF: 0.288 AC: 608 AN: 2112

Alfa AF: 0.333 Hom.: 36876

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
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs12771728; hg19: chr10-89355313;