rs7944706

Positions:

• chr11-10309764-G-A

Variant summary

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

The ENST00000527261.5(AMPD3):​n.361+1091G>A variant causes a intron change. The variant allele was found at a frequency of 0.384 in 152,050 control chromosomes in the GnomAD database, including 11,713 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 0.38 (11713 hom., cov: 33)
• Consequence: AMPD3 ENST00000527261.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.06

Genes affected

AMPD3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAND1.11	NR_103765.1	n.361+1091G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AMPD3	ENST00000527261.5	n.361+1091G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58376 AN: 151930 Hom.: 11715 Cov.: 33

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.384 AC: 58376 AN: 152050 Hom.: 11713 Cov.: 33 AF XY: 0.385 AC XY: 28582 AN XY: 74318

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.421

Alfa AF: 0.428 Hom.: 16060

Bravo AF: 0.370

Asia WGS AF: 0.453 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	20
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7944706; hg19: chr11-10331311;